################################################################ ## Test the rsat subcommands targets: @echo "Targets" @echo " targets list targets of this makefile" @echo " all run all the targets (may take some time)" @echo " download_demo_files Download demo files from the github repository" @echo " list_param list parameters" @echo " randseq random-seq" @echo " purgeseq purge-sequence" @echo " download_jaspar download jaspar PSSM collection" @echo " sequence_lengths sequence-lengths" @echo " classfreq classfreq" @echo " xygraph XYgraph" @echo " retrieve_matrix retrieve-matrix" @echo " convert_matrix convert-matrix" @echo " compare_matrices compare-matrices" @echo " matrix_clustering matrix-clustering with 2 collections (peak-motifs versus Jaspar ref)" @echo " oligos oligo-analysis" @echo " positions position-analysis" @echo " assembly pattern-assembly" @echo " matrix_from_patterns matrix-from-patterns" @echo " create_background create-background-model" @echo " matrix_distrib matrix-distrib" @echo " matrix_quality matrix-quality" @echo " peakmo peak-motifs" @echo " download_organism download-organism" @echo " supported_local supported-organisms" @echo " supported_ensembl supported-organisms-ensembl -db ensembl" @echo " supported_ensemblg supported-organisms-ensembl -db ensemblgenomes" @echo " supported_ucsc supported-organisms-ucsc" @echo " gene_info gene-info" @echo " add_gene_info add-gene-info" @echo " retrieve_seq retrieve-seq" @echo " fetch_sequences fetch-sequences" ################################################################ ## List global parameters V=1 RESULT_DIR=rsat_subcommand_results list_param: @echo "rsat path `which rsat`" @echo " RESULT_DIR ${RESULT_DIR}" ################################################################ ## Run all targets all: targets list_param download_demo_files randseq purgeseq download_jaspar sequence_lengths classfreq xygraph retrieve_matrix convert_matrix compare_matrices oligos positions assembly matrix_from_patterns create_background matrix_distrib matrix_quality peakmo download_organism supported_local supported_ensembl supported_ensemblg supported_ucsc gene_info add_gene_info retrieve_seq fetch_sequences ################################################################ ## Download demo files from the github repository DEMO_URL=https://github.com/rsa-tools/demo_files.git DEMO_FILES=demo_files download_demo_files: @echo "Downloading demo files from git repository" git clone ${DEMO_URL} @echo " DEMO_FILES ${DEMO_FILES}" ################################################################ ## Generate random sequences RANDSEQ_DIR=${RESULT_DIR}/random-seq_result RANDSEQ=${RANDSEQ_DIR}/randseq_l1000_n10.fasta randseq: @echo "Testing random-seq" @mkdir -p ${RANDSEQ_DIR} @echo " RANDSEQ_DIR ${RANDSEQ_DIR}" @echo " Generating random sequences" rsat random-seq -l 1000 -n 10 -seed 123 -o ${RANDSEQ} @echo " RANDSEQ ${RANDSEQ}" # md5sum ${RANDSEQ} > ${RANDSEQ}.md5 # @echo " md5sum ${RANDSEQ}.md5" ################################################################ ## Download JASPAR non-redundant vertebrate collection JASPAR_FILE=JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf JASPAR_URL=http://teaching.rsat.eu/motif_databases/JASPAR/Jaspar_2020/nonredundant/${JASPAR_FILE} JASPAR_DIR=${RESULT_DIR}/data/jaspar JASPAR=${JASPAR_DIR}/${JASPAR_FILE} download_jaspar: @echo "Downloading JASPAR NR vertebrates" @mkdir -p ${JASPAR_DIR} @if [ -f ${JASPAR} ] ; \ then echo " JASPAR file already there"; \ else wget --no-clobber ${JASPAR_URL} -O ${JASPAR}; \ fi @echo " JASPAR ${JASPAR}" ################################################################ ## retrieve-matrix test ## Retrieve selected matrices from JASPAR RETRIEVE_MATRIX_DIR=${RESULT_DIR}/retrieve-matrix_result SOCT_MATRIX_BASENAME=sox-oct_matrices SOCT_MATRICES=${RETRIEVE_MATRIX_DIR}/${SOCT_MATRIX_BASENAME}.tf retrieve_matrix: download_jaspar create_background @echo "Testing retrieve-matrix" @mkdir -p ${RETRIEVE_MATRIX_DIR} rsat retrieve-matrix -v ${V} -i ${JASPAR} -id POU5F1 -id SOX2 -id Pou5f1::Sox2 \ -o ${SOCT_MATRICES} @echo " SOCT_MATRICES ${SOCT_MATRICES}" ################################################################ ## convert-matrix (including the generation of logos) CONVERT_MATRIX_DIR=${RESULT_DIR}/convert-matrix_result CONVERTED_SOCT_MATRICES=${CONVERT_MATRIX_DIR}/${SOCT_MATRIX_BASENAME}.tab convert_matrix: download_jaspar @echo "Testing convert-matrix" @mkdir -p ${CONVERT_MATRIX_DIR} rsat convert-matrix -v ${V} -i ${SOCT_MATRICES} -from transfac -to tab \ -return weights,margins,logo -decimals 2 \ -o ${CONVERTED_SOCT_MATRICES} @echo " CONVERTED_SOCT_MATRICES ${CONVERTED_SOCT_MATRICES}" ################################################################ ## Compare matrices MATRIX_COMPA_DIR=${RESULT_DIR}/compare-matrices_result MATRIX_COMPA=${MATRIX_COMPA_DIR}/sox-oct_vs_itself compare_matrices: retrieve_matrix @echo "Testing compare-matices" @mkdir -p ${MATRIX_COMPA_DIR} rsat compare-matrices -v ${V} -file ${SOCT_MATRICES} -format transfac \ -mode matches -distinct -strand DR \ -lth cor 0.6 -lth Ncor 0.33 -uth match_rank 50 \ -return cor,Ncor,logoDP,match_rank,matrix_id,matrix_name,width,consensus,alignments_1ton \ -o ${MATRIX_COMPA} @echo " MATRIX_COMPA_DIR ${MATRIX_COMPA_DIR}" @echo " MATRIX_COMPA ${MATRIX_COMPA}_index.html" ################################################################ ## matrix-clustering test ## ## Clustering with two matrix collections: ## 1. Motifs discovered in Sox peaks by RSAT peak-motifs ## 2. Reference motifs for SOX and OCT transcription factors in Jaspar MATRIX_CLUSTERING_DIR=${RESULT_DIR}/matrix-clustering_result CLUSTER_PREFIX=${MATRIX_CLUSTERING_DIR}/peak-motifs_vs_jaspar_SOCT CLUSTER_ERR_LOG=${CLUSTER_PREFIX}_err.txt matrix_clustering: @echo "Testing matrix-clustering" @mkdir -p ${MATRIX_CLUSTERING_DIR} @echo " MATRIX_CLUSTERING_DIR ${MATRIX_CLUSTERING_DIR}" rsat matrix-clustering -v ${V} \ -matrix 'peak-motifs' ${OLIGO_MATRICES}_count_matrices.tf transfac \ -matrix 'jaspar_soct' ${SOCT_MATRICES} transfac \ -hclust_method average -calc sum \ -title 'peak-motifs versus Jaspar Sox-Oct' \ -metric_build_tree 'Ncor' -lth w 5 -lth cor 0.6 -lth Ncor 0.4 -quick \ -label_in_treeOC name -return json,heatmap \ -o ${CLUSTER_PREFIX} 2> ${CLUSTER_ERR_LOG} @echo " CLUSTER_PREFIX ${CLUSTER_PREFIX}" @echo " CLUSTER_ERR_LOG ${CLUSTER_ERR_LOG}" ################################################################ ## Peak sequences for tests PEAK_DIR=demo_files/ChIP-seq_peaks PEAK_BASENAME=Oct4_peaks_top1000 PEAK_FILE=${PEAK_BASENAME}.fa PEAKS=${PEAK_DIR}/${PEAK_FILE} ################################################################ ## Check the lengths of the downloaded peaks PEAK_LENGTHS=${PEAKS}_lengths.tsv sequence_lengths: @echo "Testing sequence-lengths" rsat sequence-lengths -i ${PEAKS} -o ${PEAK_LENGTHS} @echo " PEAK_LENGTHS ${PEAK_LENGTHS}" ################################################################ ## Compute the distribution of peak sequence lengths with classfreq PEAK_LEN_DISTRIB=${PEAKS}_length_distrib.tsv classfreq: sequence_lengths @echo "Testing classfreq" rsat classfreq -i ${PEAK_LENGTHS} -v ${V} -ci 10 -o ${PEAK_LEN_DISTRIB} @echo " PEAK_LEN_DISTRIB ${PEAK_LEN_DISTRIB}" ################################################################ ## XYgraph: plot the distribution of peak sequence lengths PEAK_LEN_DISTRIB_GRAPH=${PEAKS}_length_distrib.png xygraph: classfreq @echo "Testing XYgraph" rsat XYgraph -i ${PEAK_LEN_DISTRIB} \ -title 'Peak length distribution' \ -xsize 800 -ysize 400 -lines \ -xcol 3 -ycol 4,5,6 -format png \ -xleg1 "Peak length" -yleg1 "Frequencies" -legend -ymin 0 \ -xgstep1 50 -xgstep2 10 \ -ygstep1 200 -ygstep2 50 \ -o ${PEAK_LEN_DISTRIB_GRAPH} @echo " PEAK_LEN_DISTRIB_GRAPH ${PEAK_LEN_DISTRIB_GRAPH}" ################################################################ ## Purge sequences to mask repeats PURGESEQ_DIR=${RESULT_DIR}/purge-sequence_result PURGED_PEAKS=${PURGESEQ_DIR}/${PEAK_BASENAME}_purged.fa purgeseq: @echo "Testing purge-seq" @mkdir -p ${PURGESEQ_DIR} @echo " PURGESEQ_DIR ${PURGESEQ_DIR}" @echo " Purging sequences" rsat purge-sequence -i ${PEAKS} -o ${PURGED_PEAKS} @echo " PURGED_PEAKS ${PURGED_PEAKS}" ################################################################ ## oligo-analysis test OLIGO_DIR=${RESULT_DIR}/oligo-analysis_result OLIGO_BASENAME=${PEAK_BASENAME}_6nt_2str_noov_sig0 OLIGO_PREFIX=${OLIGO_DIR}/${OLIGO_BASENAME} OLIGOS=${OLIGO_PREFIX}.tsv oligos: purgeseq @echo "Testing oligo-analysis" @mkdir -p ${OLIGO_DIR} rsat oligo-analysis -v ${V} -i ${PURGED_PEAKS} \ -l 6 -2str -noov \ -return occ,freq,proba,rank \ -markov 4 -lth occ_sig 0 \ -o ${OLIGOS} @echo " OLIGO_DIR ${OLIGO_DIR}" @echo " OLIGOS ${OLIGOS}" ################################################################ ## position-analysis test ## ## Includes options to cluster k-mers based on their positional ## profiles, which reveals 2 clusters: ## 1. k-mers concentrated in the middle of the peaks ## 2. k-mers avoided in the middle of the peaks ## POSITION_DIR=${RESULT_DIR}/position-analysis_result POSITION_BASENAME=${POSITION_DIR}/${PEAK_BASENAME}_6nt_ci25 POSITIONS=${POSITION_BASENAME}.tsv positions: purgeseq @echo "Testing position-analysis" @mkdir -p ${POSITION_DIR} rsat position-analysis -v ${V} -i ${PURGED_PEAKS} \ -l 6 -2str -noov -ci 25 -lth_sig 0 -lth_occ 1 \ -clust_nb 2 -max_asmb_per_cluster 2 \ -origin center -maxpos 500 -minpos -500 \ -sort -return chi,sig,rank,distrib,clusters,matrices,graphs,index \ -o ${POSITIONS} @echo " POSITION_DIR ${POSITION_DIR}" @echo " POSITIONS ${POSITIONS}" @echo " index ${POSITION_BASENAME}_index.html" @echo " graph index ${POSITION_BASENAME}_graph_index.html" ################################################################ ## Test pattern-assembly with oligos ASSEMBLY=${OLIGO_PREFIX}_assembly.txt assembly: @echo "Testing pattern-assembly" rsat pattern-assembly -v ${V} \ -i ${OLIGOS} \ -maxfl 1 -2str -subst 1 -match 5 \ -o ${ASSEMBLY} @echo " ASSEMBLY ${ASSEMBLY}" ################################################################ ## Test matrix-from-patterns OLIGO_MATRICES=${OLIGO_PREFIX}_pssm matrix_from_patterns: @echo "Testing matrix-from-patterns" rsat matrix-from-patterns -seq ${PEAKS} \ -pl ${OLIGOS} \ -sc 9 -subst 1 -maxfl 1 -match 5 -2str \ -sites -collect_method matrix-scan-quick -flanks 3 -logo \ -o ${OLIGO_MATRICES} @echo " OLIGO_MATRICES ${OLIGO_MATRICES}" @echo " PSSM (transfac format) ${OLIGO_MATRICES}_count_matrices.tf" @echo " Sites (feature format) ${OLIGO_MATRICES}_sig_sites.ft" ################################################################ ## Test create-background-model BG_MKV=1 BG_DIR=${RESULT_DIR}/background-models BG_FORMAT=oligos BG_FILE=${BG_DIR}/${PEAK_BASENAME}_bg-model_markov${BG_MKV}_${BG_FORMAT}.tsv create_background: @echo "Testing create-background-model" @mkdir -p ${BG_DIR} rsat create-background-model -v ${V} \ -i ${PEAKS} \ -markov ${BG_MKV} -out_format ${BG_FORMAT} \ -o ${BG_FILE} @echo " BG_DIR ${BG_DIR}" @echo " BG_FILE ${BG_FILE}" ################################################################ ## Test matrix-distrib MATRIX_DISTRIB_DIR=${RESULT_DIR}/matrix-distrib_result MATRIX_DISTRIB_PREFIX=${MATRIX_DISTRIB_DIR}/${SOCT_MATRIX_BASENAME}_distrib MATRIX_DISTRIB=${MATRIX_DISTRIB_PREFIX}.tsv matrix_distrib: @echo "Testing matrix-distrib" @mkdir -p ${MATRIX_DISTRIB_DIR} rsat matrix-distrib -v ${V} \ -top 1 \ -m ${SOCT_MATRICES} -matrix_format transfac \ -pseudo 1 -decimals 1 \ -bg_format ${BG_FORMAT} \ -bgfile ${BG_FILE} \ -bg_pseudo 0.01 \ -o ${MATRIX_DISTRIB} @echo " SOCT_MATRICES ${SOCT_MATRICES}" @echo " BG_FILE ${BG_FILE}" @echo " MATRIX_DISTRIB_DIR ${MATRIX_DISTRIB_DIR}" @echo " MATRIX_DISTRIB ${MATRIX_DISTRIB}" rsat XYgraph -i ${MATRIX_DISTRIB} \ -title1 "Distribution of weights" \ -title2 "Score probability" \ -xcol 1 -ycol 2 -legend -lines -pointsize 1 \ -xleg1 "Weight" \ -yleg1 "Frequency" \ -format pdf -r_plot \ -o ${MATRIX_DISTRIB_PREFIX}_weigh-distrib.pdf @echo " Weight distrib graph ${MATRIX_DISTRIB_PREFIX}_weigh-distrib.pdf" rsat XYgraph \ -i ${MATRIX_DISTRIB} \ -title1 'Distribution of weights (log scale)' \ -title2 'Score probability and P-value' \ -xcol 1 \ -ycol 2,4 \ -legend \ -lines \ -pointsize 1 -ylog \ -xleg1 'weight' -yleg1 'Frequency (log scale)' \ -r_plot \ -format pdf \ -o ${MATRIX_DISTRIB_PREFIX}_weigh-distrib_ylog.pdf @echo " Weight distrib graph (ylog) ${MATRIX_DISTRIB_PREFIX}_weigh-distrib_ylog.pdf" ################################################################ ## Test matrix-quality QUALITY_DIR=${RESULT_DIR}/matrix-quality_result QUALITY_PREFIX=${QUALITY_DIR}/${OLIGO_BASENAME}_quality matrix_quality: create_background @echo "Testing matrix-quality" @mkdir -p ${QUALITY_DIR} rsat matrix-quality -v ${V} \ -ms ${OLIGO_MATRICES}_count_matrices.tf \ -matrix_format transfac \ -seq peaks ${PEAKS} -seq_format fasta \ -bgfile ${BG_FILE} -bg_format ${BG_FORMAT} \ -kfold 10 -perm peaks 1 \ -o ${QUALITY_PREFIX} @echo " QUALITY_DIR ${QUALITY_DIR}" @echo " index file ${QUALITY_PREFIX}_synthesis.html" ################################################################ ## peak-motifs test PEAKMO_DIR=${RESULT_DIR}/peak-motifs_result PEAKMO_TASK=purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,synthesis,small_summary,scan,motifs_vs_db peakmo: download_jaspar @echo "Testing peak-motifs" @mkdir -p ${PEAKMO_DIR} @echo " Running peak-motifs" rsat peak-motifs -v 3 \ -title Oct4_Chen2008_sites_from_Jaspar \ -i ${PEAKS} \ -markov auto \ -disco oligos,positions \ -nmotifs 5 -minol 6 -maxol 6 -no_merge_lengths -2str -origin center \ -scan_markov 1 -source galaxy \ -prefix peak-motifs -noov -img_format png \ -motif_db JASPAR transfac ${JASPAR} \ -task ${PEAKMO_TASK} \ -outdir ${PEAKMO_DIR} \ &> ${PEAKMO_DIR}/peak-motifs_log.txt @echo " PEAK_MO_DIR ${PEAKMO_DIR}" @echo " Log file ${PEAKMO_DIR}/peak-motifs_log.txt" @echo " Result page ${PEAKMO_DIR}/peak-motifs_synthesis.html" ################################################################ ## Download an organism from an RSAT server ORGANISM=Saccharomyces_cerevisiae download_organism: @echo "Testing download-organism" @echo " ORGANISM ${ORGANISM}" rsat download-organism -v ${V} -org ${ORGANISM} ################################################################ ## List the organisms supported on the local RSAT instance SUPPORTED_DIR=${RESULT_DIR}/supported-organisms-x_results SUPPORTED_LOCAL=${SUPPORTED_DIR}/supported-organisms_local.tsv supported_local: @echo "Testing supported-organisms" @mkdir -p ${SUPPORTED_DIR} @echo " SUPPORTED_DIR ${SUPPORTED_DIR}" rsat supported-organisms -v ${V} -o ${SUPPORTED_LOCAL} @echo " SUPPORTED_LOCAL ${SUPPORTED_LOCAL}" ################################################################ ## List the organisms supported at ensembl (http://ensembl.org) ENSEMBL_DB=ensembl SUPPORTED_ENSEMBL=${SUPPORTED_DIR}/supported-organisms-ensembl_db-${ENSEMBL_DB}.tsv supported_ensembl: @echo "Testing supported-organisms-ensembl" @mkdir -p ${SUPPORTED_DIR} @echo " SUPPORTED_DIR ${SUPPORTED_DIR}" rsat supported-organisms-ensembl -v ${V} -db ensembl -o ${SUPPORTED_ENSEMBL} @echo " ENSEMBL_DB ${ENSEMBL_DB}" @echo " SUPPORTED_ENSEMBL ${SUPPORTED_ENSEMBL}" @echo " Number of organisms in Ensembl `grep -v ';' ${SUPPORTED_ENSEMBL} | wc -l`" ################################################################ ## List the organisms supported at ensembl (http://ensembl.org) SUPPORTED_ENSEMBLGENOMES=${SUPPORTED_DIR}/supported-organisms-ensembl_db-ensemblgenomes.tsv supported_ensemblg: @echo "Testing supported-organisms-ensembl with ensemblgenomes" @mkdir -p ${SUPPORTED_DIR} @echo " SUPPORTED_DIR ${SUPPORTED_DIR}" rsat supported-organisms-ensembl -v ${V} -db ensemblgenomes -o ${SUPPORTED_ENSEMBLGENOMES} @echo " SUPPORTED_ENSEMBLGENOMES ${SUPPORTED_ENSEMBLGENOMES}" @echo " Number of organisms in EnsemblGenomes `grep -v ';' ${SUPPORTED_ENSEMBLGENOMES} | wc -l`" ################################################################ ## List the organisms supported at ensembl (http://ensembl.org) ## NOTE: THIS SCRIPT IS STILL NOT FINISHED (JvH, 2020-01-04) TAXID=4751 SUPPORTED_ENSEMBLGENOMES_TAXID=${SUPPORTED_DIR}/supported-organisms-ensemblgenomes_branch${TAXID}.tsv supported_ensemblg_taxid: @echo "Testing supported-organisms-ensemblgenomes" @mkdir -p ${SUPPORTED_DIR} @echo " SUPPORTED_DIR ${SUPPORTED_DIR}" rsat supported-organisms-ensemblgenomes -v ${V} \ -query_type branch -q ${TAXID} \ -o ${SUPPORTED_ENSEMBLGENOMES_TAXID} @echo " TAXID ${TAXID}" @echo " SUPPORTED_ENSEMBLGENOMES_TAXID ${SUPPORTED_ENSEMBLGENOMES_TAXID}" ################################################################ ## List the organisms supported at UCSC genome browser (https://genome.ucsc.edu/) SUPPORTED_UCSC=${SUPPORTED_DIR}/supported-organisms-ucsc.tsv supported_ucsc: @echo "Testing supported-organisms-ucsc" @mkdir -p ${SUPPORTED_DIR} @echo " SUPPORTED_DIR ${SUPPORTED_DIR}" rsat supported-organisms-ucsc -v ${V} -o ${SUPPORTED_UCSC} @echo " SUPPORTED_UCSC ${SUPPORTED_UCSC}" @echo " Number of organisms `grep -v ';' ${SUPPORTED_UCSC} | wc -l`" ################################################################ ## Get inforamtion about genes for an organism installed locally GENE_INFO_DIR=${RESULT_DIR}/gene-info_result FEATTYPE=gene GENE_INFO=${GENE_INFO_DIR}/${ORGANISM}_MET_${FEATTYPE}_info.tsv gene_info: @echo "Testing gene-info" @mkdir -p ${GENE_INFO_DIR} @echo " GENE_INFO_DIR ${GENE_INFO_DIR}" rsat gene-info -org ${ORGANISM} -q 'MET\d+' -feattype ${FEATTYPE} -o ${GENE_INFO} @echo " GENE_INFO ${GENE_INFO}" ################################################################ ## Add user-specified information to a gene table GENE_INFO_ADDED=${GENE_INFO_DIR}/${ORGANISM}_MET_${FEATTYPE}_info-added.tsv add_gene_info: gene_info @echo "Testing add-gene-info" rsat add-gene-info -i ${GENE_INFO} \ -org ${ORGANISM} \ -info upstr_size,downstr_size,names \ -col 1 -feattype ${FEATTYPE} \ -o ${GENE_INFO_ADDED} @echo " GENE_INFO_ADDED ${GENE_INFO_ADDED}" ################################################################ ## Retrieve sequences from a locally installed organism RETRIEVE_SEQ_DIR=${RESULT_DIR}/retrieve-seq_result RETRIEVED_SEQ=${RETRIEVE_SEQ_DIR}/${ORGANISM}_MET_${FEATTYPE}_upstream-noorf.fasta retrieve_seq: gene_info @echo "Testing retrieve-seq" @mkdir -p ${RETRIEVE_SEQ_DIR} @echo " RETRIEVE_SEQ_DIR RETRIEVE_${SEQ_DIR}" rsat retrieve-seq -org ${ORGANISM} \ -i ${GENE_INFO} \ -type upstream -noorf -feattype ${FEATTYPE} -label id,name \ -o ${RETRIEVED_SEQ} @echo " RETRIEVED_SEQ ${RETRIEVED_SEQ}" ################################################################ ## Fetch sequences from UCSC genome browser FETCHED_SEQ_DIR=${RESULT_DIR}/fetch-sequences_result CEBPA_PEAKS_BASENAME=fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks CEBPA_PEAKS_COORD_URL=http://metazoa.rsat.eu/demo_files/${CEBPA_PEAKS_BASENAME}.bed CEBPA_PEAKS_BED=${FETCHED_SEQ_DIR}/${CEBPA_PEAKS_BASENAME}.bed CEBPA_PEAKS_SEQ=${FETCHED_SEQ_DIR}/${CEBPA_PEAKS_BASENAME}.fasta fetch_sequences: @echo "Testing fetch-sequences" @mkdir -p ${FETCHED_SEQ_DIR} @echo " FETCHED_SEQ_DIR ${FETCHED_SEQ_DIR}" @echo " CEBPA_PEAKS_COORD_URL ${CEBPA_PEAKS_COORD_URL}" wget --no-clobber ${CEBPA_PEAKS_COORD_URL} -O ${CEBPA_PEAKS_BED} @echo " CEBPA_PEAKS_BED ${CEBPA_PEAKS_BED}" rsat fetch-sequences -i ${CEBPA_PEAKS_BED} -genome mm9 -o ${CEBPA_PEAKS_SEQ} @echo " CEBPA_PEAKS_SEQ ${CEBPA_PEAKS_SEQ}"