"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!perl -e '$count=0; $len=0; while(<>) {s/\\r?\\n//; s/\\t/ /g; if (s/^>//) { if ($. != 1) {print \"\\n\"} s/ |$/\\t/; $count++; $_ .= \"\\t\";} else {s/ //g; $len += length($_)} print $_;} print \"\\n\"; warn \"\\nConverted $count FASTA records in $. lines to tabular format\\nTotal sequence length: $len\\n\\n\";' /Volumes/web/cnidarian/fish546_14_Trinity.fasta > /Volumes/web/cnidarian/fish546_14_Trinity.tab"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Converted 113679 FASTA records in 2442378 lines to tabular format\r\n",
"Total sequence length: 136406223\r\n",
"\r\n"
]
}
],
"prompt_number": 78
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!perl -e '$col = 2;' -e 'while (<>) { s/\\r?\\n//; @F = split /\\t/, $_; $len = length($F[$col]); print \"$_\\t$len\\n\" } warn \"\\nAdded column with length of column $col for $. lines.\\n\\n\";' /Volumes/web/cnidarian/fish546_14_Trinity.tab > /Volumes/web/cnidarian/fish546_14_Trinity_ls_length2.tab"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"Added column with length of column 2 for 113679 lines.\r\n",
"\r\n"
]
}
],
"prompt_number": 99
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head -2 /Volumes/web/cnidarian/fish546_14_Trinity_ls_length2.tab"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"comp0_c0_seq1\tlen=526 path=[4411:0-525]\tTCTGTGCCGATATATATATACATGTATCTATGCACAGTCATGTTTTATCGAGTACGACTGTAAAAAAGATCCAAAGTATACTCAAAAAATCTTCAGCAAGTGAGTCCATTTGAGTATGAGAATGATATTATCAAAGTTTTAAAACAATTTAGAGCATAGAGGTTGAGTCCGTGTATGAAAATGTGCTCAAAAAAGTAAATATAACTTCCAGGACAATTATTTTTACCGGCGTCTACTTGTATCTGTACGTATATTAAAAGTCTTAACGGCCACTGAACGAGCCAGCCTATTTATAAACTTGTTAACGCTTCCTTAAATGGCTGTAACTGAAGCTCCAAGCAAGTACTTAGCTAGAAAACACCCAGACGTACGTAAAAGTTTCCTTATTTACTGAAAATTTAAATGTATTCACCCAGTAGCACCCGGGGCCTTGATGAGGCCACGATAAATCTGCTTTTCAACAACCATAATGATTTGTTAATTCATAAGAAACACGCTCATGTATAGACTTCGATTTCAGGATAAG\t526\r\n",
"comp1_c0_seq1\tlen=265 path=[1100:0-54 2691:55-264]\tGGGGAATTCAGCTAACATACCTCGATGATGAGGGGGAGCCGTCCTGTCAAAACTCCAATAATCTGAATTATACACTGCTGAAGCACTTAACACGTCAAGATGTGGGGTGTGCCTTAGATACAACATCTACAAAAATAAATCTAGACACTGACCTGGACTCCAGAGCCGATACAGACACTGTCCTTACTGAAATTACCAAACCTGGCAAGTATTGAACGTGTACCAAAACTTATAGATTTTGTATATGGTATTAATTTCTCTGGTG\t265\r\n"
]
}
],
"prompt_number": 100
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from pandas import *\n",
"\n",
"# read data from data file into a pandas DataFrame \n",
"la = read_table(\"http://eagle.fish.washington.edu/cnidarian/fish546_14_Trinity_ls_length2.tab\", # name of the data file\n",
" #sep=\",\", # what character separates each column?\n",
" na_values=[\"\", \" \"]) # what values should be considered \"blank\" values?"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 101
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"la.head()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
"\n",
"<class 'pandas.core.frame.DataFrame'>\n",
"Int64Index: 5 entries, 0 to 4\n",
"Data columns (total 4 columns):\n",
"comp0_c0_seq1 5 non-null values\n",
"len=526 path=[4411:0-525] 5 non-null values\n",
"TCTGTGCCGATATATATATACATGTATCTATGCACAGTCATGTTTTATCGAGTACGACTGTAAAAAAGATCCAAAGTATACTCAAAAAATCTTCAGCAAGTGAGTCCATTTGAGTATGAGAATGATATTATCAAAGTTTTAAAACAATTTAGAGCATAGAGGTTGAGTCCGTGTATGAAAATGTGCTCAAAAAAGTAAATATAACTTCCAGGACAATTATTTTTACCGGCGTCTACTTGTATCTGTACGTATATTAAAAGTCTTAACGGCCACTGAACGAGCCAGCCTATTTATAAACTTGTTAACGCTTCCTTAAATGGCTGTAACTGAAGCTCCAAGCAAGTACTTAGCTAGAAAACACCCAGACGTACGTAAAAGTTTCCTTATTTACTGAAAATTTAAATGTATTCACCCAGTAGCACCCGGGGCCTTGATGAGGCCACGATAAATCTGCTTTTCAACAACCATAATGATTTGTTAATTCATAAGAAACACGCTCATGTATAGACTTCGATTTCAGGATAAG 5 non-null values\n",
"526 5 non-null values\n",
"dtypes: int64(1), object(3)\n",
"
"
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 103,
"text": [
" comp0_c0_seq1 len=526 path=[4411:0-525] \\\n",
"0 comp1_c0_seq1 len=265 path=[1100:0-54 2691:55-264] \n",
"1 comp2_c0_seq1 len=284 path=[8218:0-178 713:179-283] \n",
"2 comp3_c0_seq1 len=591 path=[36159:0-115 8073:116-590] \n",
"3 comp3_c0_seq2 len=869 path=[3:0-393 8073:394-868] \n",
"4 comp4_c0_seq1 len=693 path=[13985:0-396 29716:397-409 22754:... \n",
"\n",
" TCTGTGCCGATATATATATACATGTATCTATGCACAGTCATGTTTTATCGAGTACGACTGTAAAAAAGATCCAAAGTATACTCAAAAAATCTTCAGCAAGTGAGTCCATTTGAGTATGAGAATGATATTATCAAAGTTTTAAAACAATTTAGAGCATAGAGGTTGAGTCCGTGTATGAAAATGTGCTCAAAAAAGTAAATATAACTTCCAGGACAATTATTTTTACCGGCGTCTACTTGTATCTGTACGTATATTAAAAGTCTTAACGGCCACTGAACGAGCCAGCCTATTTATAAACTTGTTAACGCTTCCTTAAATGGCTGTAACTGAAGCTCCAAGCAAGTACTTAGCTAGAAAACACCCAGACGTACGTAAAAGTTTCCTTATTTACTGAAAATTTAAATGTATTCACCCAGTAGCACCCGGGGCCTTGATGAGGCCACGATAAATCTGCTTTTCAACAACCATAATGATTTGTTAATTCATAAGAAACACGCTCATGTATAGACTTCGATTTCAGGATAAG \\\n",
"0 GGGGAATTCAGCTAACATACCTCGATGATGAGGGGGAGCCGTCCTG... \n",
"1 GCGAGATGTACATGTAACCCAAATTAAGCATGTTAAATCATTAGCT... \n",
"2 CCAATCTTTAGTAAGTTTATATTAATTTCTATGATAATATTTGAAA... \n",
"3 GTATAATGCTGACCTTGAACATTTTCATCGCTTCATGACTGACGTT... \n",
"4 TGTTTCTTGTTATAATTATTGTGTACGTTGTTTCGTATCTGACGTC... \n",
"\n",
" 526 \n",
"0 265 \n",
"1 284 \n",
"2 591 \n",
"3 869 \n",
"4 693 "
]
}
],
"prompt_number": 103
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"la ['526'].hist(bins=1000);\n",
"#Axis limits are changed using the axis([xmin, xmax, ymin, ymax]) function.\n",
"plt.axis([0, 4000, 0, 11000])\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 113,
"text": [
"[0, 4000, 0, 11000]"
]
},
{
"metadata": {},
"output_type": "display_data",
"png": 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33347Zs2ahVAopNUxnSgjoN/xvO222wAA/f39GBwcRFpamlbH8kY5Af2OZ2dn\nJw4fPox169ZZ2RJxPLUuFom4B+NmOBwOLFy4EA899BDefvttAEB3dzdcLhcAwOVyobu7GwDQ1dU1\n6qquRGe/2VzXz3e73QnL+9Zbb6GgoACVlZXW6bMuOc+fP48zZ85g7ty52h7T4Yzz5s0DoN/xHBoa\ngt/vh8vlsobOdDyW4+UE9DuemzZtwmuvvYakpGsf34k4nloXC9W3q8fro48+wpkzZ3DkyBH89re/\nxYcffjhqebRb7O3an6m49V+V9evXo729HWfPnsU999yDF154we5IlkuXLmH16tXYsWMH7rjjjlHL\ndDmmly5dwhNPPIEdO3bg9ttv1/J4JiUl4ezZs+js7MSJEydw/PjxUct1OZbX5wwEAtodz/fffx/p\n6ekoLCyc8JaCqTqeWheLydyDkUj33HMPAODuu+/Gj3/8Y5w6dQoulwsXLlwAAITDYaSnpwMYm72z\nsxNutzthWW8ml8fjgdvtRmdnZ8LzpqenW3+5161bZw3V2Z1zYGAAq1evxpo1a7Bq1SoA+h3T4YxP\nP/20lVHX4wkAd955J370ox+hpaVFu2M5Xs7m5mbtjudf//pXHDp0CPfeey/KysrwwQcfYM2aNYk5\nnso7LwoNDAzIfffdJ+3t7XLlyhVbG9zffPONXLx4UURELl26JI888oj88Y9/lM2bN0ttba2IiNTU\n1IxpLF25ckXa2trkvvvusxpLU6G9vX1Mg/tmcxUVFcnJkydlaGhoyhpz1+fs6uqyfv71r38tZWVl\ntuccGhqSNWvWyPPPPz9qvk7HdKKMuh3Pf//73/L111+LiMjly5flsccek2PHjml1LG+UMxwOW6/R\n4XiOFAgEZPny5SKSmL+bWhcLEZHDhw9Ldna2ZGZmyvbt223L0dbWJgUFBVJQUCCzZ8+2snz11Vey\nYMEC8fl8UlJSYv2FExGprq6WzMxMycnJkcbGxinL9uSTT8o999wjKSkp4vF45J133okpV3Nzs8yZ\nM0cyMzPlF7/4xZTnrK+vlzVr1kh+fr7cf//98vjjj8uFCxdsz/nhhx+Kw+GQgoIC8fv94vf75ciR\nI1od0/EyHj58WLvj+cknn0hhYaEUFBRIfn6+vPrqqyIS278bO3LqdjxHCgQC1tVQiTieDhE+S4OI\niG5M654FERHpgcWCiIiiYrEgIqKoWCyIiCgqFgsiIoqKxYKIiKL6fxHE39grzxxZAAAAAElFTkSu\nQmCC\n",
"text": [
""
]
}
],
"prompt_number": 113
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!perl /Users/sr320/Desktop/trinityrnaseq_r20131110/util/TrinityStats.pl /Volumes/web/cnidarian/fish546_14_Trinity.fasta\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"\r\n",
"################################\r\n",
"## Counts of transcripts, etc.\r\n",
"################################\r\n",
"Total trinity transcripts:\t113679\r\n",
"Total trinity components:\t69205\r\n",
"Percent GC: 40.03\r\n",
"\r\n",
"########################################\r\n",
"Stats based on ALL transcript contigs:\r\n",
"########################################\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\tContig N10: 6804\r\n",
"\tContig N20: 4912\r\n",
"\tContig N30: 3808\r\n",
"\tContig N40: 2996\r\n",
"\tContig N50: 2375\r\n",
"\r\n",
"\tMedian contig length: 572\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\tAverage contig: 1199.92\r\n",
"\tTotal assembled bases: 136406223\r\n",
"\r\n",
"\r\n",
"#####################################################\r\n",
"## Stats based on ONLY LONGEST ISOFORM per COMPONENT:\r\n",
"#####################################################\r\n",
"\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\tContig N10: 5174\r\n",
"\tContig N20: 3631\r\n",
"\tContig N30: 2726\r\n",
"\tContig N40: 2099\r\n",
"\tContig N50: 1604\r\n",
"\r\n",
"\tMedian contig length: 382\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\tAverage contig: 823.03\r\n",
"\tTotal assembled bases: 56957585\r\n",
"\r\n",
"\r\n",
"\r\n"
]
}
],
"prompt_number": 120
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Running CD-Hit on IPlant\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd /Volumes/web/cnidarian/"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/web/cnidarian\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!curl -o 'fishfe6_oCD-HITout.fa' 'http://de.iplantcollaborative.org/dl/d/26cb3b68-ea18-4a9f-a723-247e03c0166a/CD-HITout.fa'"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\r\n",
" Dload Upload Total Spent Left Speed\r\n",
"\r",
" 0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 1150 0 1150 0 0 359 0 --:--:-- 0:00:03 --:--:-- 1046"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 161k 0 161k 0 0 47063 0 --:--:-- 0:00:03 --:--:-- 114k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 514k 0 514k 0 0 112k 0 --:--:-- 0:00:04 --:--:-- 207k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 836k 0 836k 0 0 151k 0 --:--:-- 0:00:05 --:--:-- 243k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 1189k 0 1189k 0 0 181k 0 --:--:-- 0:00:06 --:--:-- 266k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 1476k 0 1476k 0 0 194k 0 --:--:-- 0:00:07 --:--:-- 336k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 1798k 0 1798k 0 0 210k 0 --:--:-- 0:00:08 --:--:-- 325k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 2145k 0 2145k 0 0 223k 0 --:--:-- 0:00:09 --:--:-- 325k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 2468k 0 2468k 0 0 233k 0 --:--:-- 0:00:10 --:--:-- 324k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 2785k 0 2785k 0 0 242k 0 --:--:-- 0:00:11 --:--:-- 323k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 3138k 0 3138k 0 0 249k 0 --:--:-- 0:00:12 --:--:-- 331k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 3462k 0 3462k 0 0 255k 0 --:--:-- 0:00:13 --:--:-- 332k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 3810k 0 3810k 0 0 261k 0 --:--:-- 0:00:14 --:--:-- 332k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 4130k 0 4130k 0 0 265k 0 --:--:-- 0:00:15 --:--:-- 332k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 4482k 0 4482k 0 0 270k 0 --:--:-- 0:00:16 --:--:-- 334k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 4772k 0 4772k 0 0 272k 0 --:--:-- 0:00:17 --:--:-- 331k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 5129k 0 5129k 0 0 276k 0 --:--:-- 0:00:18 --:--:-- 333k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 5487k 0 5487k 0 0 280k 0 --:--:-- 0:00:19 --:--:-- 335k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 5802k 0 5802k 0 0 282k 0 --:--:-- 0:00:20 --:--:-- 336k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 6159k 0 6159k 0 0 285k 0 --:--:-- 0:00:21 --:--:-- 335k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 6437k 0 6437k 0 0 285k 0 --:--:-- 0:00:22 --:--:-- 333k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 6797k 0 6797k 0 0 288k 0 --:--:-- 0:00:23 --:--:-- 332k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 7114k 0 7114k 0 0 290k 0 --:--:-- 0:00:24 --:--:-- 328k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 7471k 0 7471k 0 0 292k 0 --:--:-- 0:00:25 --:--:-- 330k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 7791k 0 7791k 0 0 293k 0 "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"--:--:-- 0:00:26 --:--:-- 331k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 8143k 0 8143k 0 0 295k 0 --:--:-- 0:00:27 --:--:-- 338k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 8495k 0 8495k 0 0 297k 0 --:--:-- 0:00:28 --:--:-- 337k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 8782k 0 8782k 0 0 297k 0 --:--:-- 0:00:29 --:--:-- 333k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 9161k 0 9161k 0 0 299k 0 --:--:-- 0:00:30 --:--:-- 339k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 9487k 0 9487k 0 0 301k 0 --:--:-- 0:00:31 --:--:-- 338k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 9775k 0 9775k 0 0 300k 0 --:--:-- 0:00:32 --:--:-- 329k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 9.8M 0 9.8M 0 0 301k 0 --:--:-- 0:00:33 --:--:-- 328k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r",
"100 10.2M 0 10.2M 0 0 302k "
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 0 --:--:-- 0:00:34 --:--:-- 336k"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
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">comp0_c0_seq1 len=526 path=[4411:0-525]\r\n",
"TCTGTGCCGATATATATATACATGTATCTATGCACAGTCATGTTTTATCGAGTACGACTG\r\n",
"TAAAAAAGATCCAAAGTATACTCAAAAAATCTTCAGCAAGTGAGTCCATTTGAGTATGAG\r\n",
"AATGATATTATCAAAGTTTTAAAACAATTTAGAGCATAGAGGTTGAGTCCGTGTATGAAA\r\n",
"ATGTGCTCAAAAAAGTAAATATAACTTCCAGGACAATTATTTTTACCGGCGTCTACTTGT\r\n",
"ATCTGTACGTATATTAAAAGTCTTAACGGCCACTGAACGAGCCAGCCTATTTATAAACTT\r\n",
"GTTAACGCTTCCTTAAATGGCTGTAACTGAAGCTCCAAGCAAGTACTTAGCTAGAAAACA\r\n",
"CCCAGACGTACGTAAAAGTTTCCTTATTTACTGAAAATTTAAATGTATTCACCCAGTAGC\r\n",
"ACCCGGGGCCTTGATGAGGCCACGATAAATCTGCTTTTCAACAACCATAATGATTTGTTA\r\n",
"ATTCATAAGAAACACGCTCATGTATAGACTTCGATTTCAGGATAAG\r\n"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!cat fishfe6_oCD-HITout.fa | awk '((NR-2)%4==0){read=$1;total++;count[read]++}END{for(read in count){if(!max||count[read]>max) {max=count[read];maxRead=read};if(count[read]==1){unique++}};print total,unique,unique*100/total,maxRead,count[maxRead],count[maxRead]*100/total}'\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"340785 321619 94.3759 G 126 0.0369735\r\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!fgrep -c \">\" fishfe6_oCD-HITout.fa"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"81885\r\n"
]
}
],
"prompt_number": 6
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Bowtie on IPlant to get alignment"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head BowtieOut.sam"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"^C\r\n"
]
}
],
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!/Volumes/Bay3/Software/BSMAP/bsmap-2.74/samtools/samtools -help"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"[main] unrecognized command '-help'\r\n"
]
}
],
"prompt_number": 13
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Tophat on IPlant to get alignment"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"Visualized in IGV"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"mpileup on IPlant"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"![ss](http://eagle.fish.washington.edu/cnidarian/skitch/Screenshot_2_11_14_9_00_AM_18AA8EAD.png)"
]
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"-- Trinity on hummingbird\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!/usr/local/bioinformatics/trinity/Trinity.pl"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"\r\n",
"###############################################################################\r\n",
"#\r\n",
"# ______ ____ ____ ____ ____ ______ __ __\r\n",
"# | || \\ | || \\ | || || | |\r\n",
"# | || D ) | | | _ | | | | || | |\r\n",
"# |_| |_|| / | | | | | | | |_| |_|| ~ |\r\n",
"# | | | \\ | | | | | | | | | |___, |\r\n",
"# | | | . \\ | | | | | | | | | | |\r\n",
"# |__| |__|\\_||____||__|__||____| |__| |____/\r\n",
"#\r\n",
"###############################################################################\r\n",
"#\r\n",
"# Required:\r\n",
"#\r\n",
"# --seqType :type of reads: ( fa, or fq )\r\n",
"#\r\n",
"# --JM :(Jellyfish Memory) number of GB of system memory to use for \r\n",
"# k-mer counting by jellyfish (eg. 10G) *include the 'G' char \r\n",
"#\r\n",
"# If paired reads:\r\n",
"# --left :left reads, one or more (separated by space)\r\n",
"# --right :right reads, one or more (separated by space)\r\n",
"#\r\n",
"# Or, if unpaired reads:\r\n",
"# --single :single reads, one or more (note, if single file contains pairs, can use flag: --run_as_paired )\r\n",
"#\r\n",
"####################################\r\n",
"## Misc: #########################\r\n",
"#\r\n",
"# --SS_lib_type :Strand-specific RNA-Seq read orientation.\r\n",
"# if paired: RF or FR,\r\n",
"# if single: F or R. (dUTP method = RF)\r\n",
"# See web documentation.\r\n",
"#\r\n",
"# --output :name of directory for output (will be\r\n",
"# created if it doesn't already exist)\r\n",
"# default( \"/Users/steven/Dropbox/Steven/ipython_nb/fish546/trinity_out_dir\" )\r\n",
"# --CPU :number of CPUs to use, default: 2\r\n",
"# --min_contig_length :minimum assembled contig length to report\r\n",
"# (def=200)\r\n",
"# --genome_guided :set to genome guided mode, only retains assembly fasta file.\r\n",
"# --jaccard_clip :option, set if you have paired reads and\r\n",
"# you expect high gene density with UTR\r\n",
"# overlap (use FASTQ input file format\r\n",
"# for reads).\r\n",
"# (note: jaccard_clip is an expensive\r\n",
"# operation, so avoid using it unless\r\n",
"# necessary due to finding excessive fusion\r\n",
"# transcripts w/o it.)\r\n",
"# \r\n",
"# --prep :Only prepare files (high I/O usage) and stop before kmer counting.\r\n",
"#\r\n",
"# --no_cleanup :retain all intermediate input files.\r\n",
"# --full_cleanup :only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta\r\n",
"#\r\n",
"# --cite :show the Trinity literature citation\r\n",
"#\r\n",
"# --version :reports Trinity version (Trinityrnaseq_r20131110) and exits.\r\n",
"#\r\n",
"####################################################\r\n",
"# Inchworm and K-mer counting-related options: #####\r\n",
"#\r\n",
"# --min_kmer_cov :min count for K-mers to be assembled by\r\n",
"# Inchworm (default: 1)\r\n",
"# --inchworm_cpu :number of CPUs to use for Inchworm, default is min(6, --CPU option)\r\n",
"#\r\n",
"# --no_run_inchworm :stop after running jellyfish, before inchworm.\r\n",
"#\r\n",
"###################################\r\n",
"# Chrysalis-related options: ######\r\n",
"#\r\n",
"# --max_reads_per_graph :maximum number of reads to anchor within\r\n",
"# a single graph (default: 200000)\r\n",
"# --no_run_chrysalis :stop Trinity after Inchworm and before\r\n",
"# running Chrysalis\r\n",
"# --no_run_quantifygraph :stop Trinity just before running the\r\n",
"# parallel QuantifyGraph computes, to\r\n",
"# leverage a compute farm and massively\r\n",
"# parallel execution..\r\n",
"#\r\n",
"# --chrysalis_output :name of directory for chrysalis output (will be\r\n",
"# created if it doesn't already exist)\r\n",
"# default( \"chrysalis\" )\r\n",
"#\r\n",
"# --no_bowtie :dont run bowtie to use pair info in chrysalis clustering.\r\n",
"#\r\n",
"#####################################\r\n",
"### Butterfly-related options: ####\r\n",
"#\r\n",
"# --bfly_opts :additional parameters to pass through to butterfly\r\n",
"# (see butterfly options: java -jar Butterfly.jar ).\r\n",
"# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).\r\n",
"#\r\n",
"# //////////////////////////////////\r\n",
"# Alternative reconstruction modes:\r\n",
"# Default mode is the 'regular' Butterfly transcript reconstruction by graph node extension.\r\n",
"#\r\n",
"# --PasaFly PASA-like algorithm for maximally-supported isoforms (conservative reconstructions, fewer isoforms)\r\n",
"# or\r\n",
"# --CuffFly Cufflinks-like algorithm to report minimum transcripts (fewest isoforms)\r\n",
"#\r\n",
"#\r\n",
"# Butterfly read-pair grouping settings (used for all reconstruction modes to define 'pair paths'):\r\n",
"#\r\n",
"# --group_pairs_distance :maximum length expected between fragment pairs (default: 500)\r\n",
"# (reads outside this distance are treated as single-end)\r\n",
"#\r\n",
"# ///////////////////////////////////////////////\r\n",
"# Butterfly default reconstruction mode settings. (no CuffFly or PasaFly custom settings are currently available).\r\n",
"# \r\n",
"# --path_reinforcement_distance :minimum overlap of reads with growing transcript \r\n",
"# path (default: PE: 75, SE: 25)\r\n",
"# Set to 1 for the most lenient path extension requirements.\r\n",
"#\r\n",
"# --triplet_lock : (increase stringency of regular butterfly reconstruction)\r\n",
"# lock triplet-supported nodes: node 'c' having read path 'A-B-C' disables 'Z-B-C' if no such read support exists.\r\n",
"#\r\n",
"# --extended_lock : (further increase the stringency of regular butterfy reconstruction) \r\n",
"# extend the triplet lock to include longer range read path information.\r\n",
"# ex. in extending path 'A-B-Z' to 'A-B-Z-D', we only find read support for 'A-B-C-D', that 'A-B-Z' extension to 'D' will be blocked.\r\n",
"# (assumes --triplet_lock)\r\n",
"#\r\n",
"# /////////////////////////////////////////\r\n",
"# Butterfly transcript reduction settings:\r\n",
"#\r\n",
"# --no_path_merging : all transcript candidates are output (including SNP variations, however, some SNPs may be unphased) \r\n",
"#\r\n",
"# By default, alternative transcript candidates are merged (in reality, discarded) if they are found to be too similar, according to the following logic:\r\n",
"#\r\n",
"# (identity=(numberOfMatches/shorterLen) > 95.0% or if we have <= 2 mismatches) and if we have internal gap lengths <= 10\r\n",
"#\r\n",
"# with parameters as:\r\n",
"# \r\n",
"# --min_per_id_same_path default: 95 min percent identity for two paths to be merged into single paths\r\n",
"# --max_diffs_same_path default: 2 max allowed differences encountered between path sequences to combine them\r\n",
"# --max_internal_gap_same_path default: 10 maximum number of internal consecutive gap characters allowed for paths to be merged into single paths.\r\n",
"#\r\n",
"# If, in a comparison between two alternative transcripts, they are found too similar, the transcript with the greatest cumulative \r\n",
"# compatible read (pair-path) support is retained, and the other is discarded.\r\n",
"#\r\n",
"#\r\n",
"# //////////////////////////////////////////////\r\n",
"# Butterfly Java and parallel execution settings.\r\n",
"#\r\n",
"# --bflyHeapSpaceMax :java max heap space setting for butterfly\r\n",
"# (default: 10G) => yields command\r\n",
"# 'java -Xmx10G -jar Butterfly.jar ... $bfly_opts'\r\n",
"# --bflyHeapSpaceInit :java initial hap space settings for\r\n",
"# butterfly (default: 1G) => yields command\r\n",
"# 'java -Xms1G -jar Butterfly.jar ... $bfly_opts'\r\n",
"# --bflyGCThreads :threads for garbage collection\r\n",
"# (default, not specified, so java decides)\r\n",
"# --bflyCPU :CPUs to use (default will be normal \r\n",
"# number of CPUs; e.g., 2)\r\n",
"# --bflyCalculateCPU :Calculate CPUs based on 80% of max_memory\r\n",
"# divided by maxbflyHeapSpaceMax\r\n",
"# --no_run_butterfly :stops after the Chrysalis stage. You'll\r\n",
"# need to run the Butterfly computes\r\n",
"# separately, such as on a computing grid.\r\n",
"# Then, concatenate all the Butterfly assemblies by running:\r\n",
"# 'find trinity_out_dir/ -name \"*allProbPaths.fasta\" \r\n",
"# -exec cat {} + > trinity_out_dir/Trinity.fasta'\r\n",
"#\r\n",
"#################################\r\n",
"# Grid-computing options: #######\r\n",
"#\r\n",
"# --grid_computing_module : Perl module in /usr/local/bioinformatics/trinityrnaseq_r20131110/PerlLibAdaptors/ \r\n",
"# that implements 'run_on_grid()' \r\n",
"# for naively parallel cmds. (eg. 'BroadInstGridRunner')\r\n",
"#\r\n",
"#\r\n",
"###############################################################################\r\n",
"#\r\n",
"# *Note, a typical Trinity command might be:\r\n",
"# Trinity.pl --seqType fq --JM 100G --left reads_1.fq --right reads_2.fq --CPU 6\r\n",
"#\r\n",
"# see: /usr/local/bioinformatics/trinityrnaseq_r20131110/sample_data/test_Trinity_Assembly/\r\n",
"# for sample data and 'runMe.sh' for example Trinity execution\r\n",
"# For more details, visit: http://trinityrnaseq.sf.net\r\n",
"#\r\n",
"###############################################################################\r\n",
"\r\n",
"\r\n",
"\r\n",
"\r\n",
"\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd /Volumes/Data/sr320_scratch/"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/Data/sr320_scratch\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"pwd"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 3,
"text": [
"u'/Volumes/Data/sr320_scratch'"
]
}
],
"prompt_number": 3
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"!/usr/local/bioinformatics/trinity/Trinity.pl -seqType fq --JM 20G --left 3filtered_106A_Female_Mix_GATCAG_L004_R1.fastq --right 3filtered_106A_Female_Mix_GATCAG_L004_R2.fastq --CPU 14 --output /Volumes/Data/sr320_scratch/trinity_out_dir "
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}