# TOBIAS Manual ## 1. ATACorrect Files are from Encode-pipele output folder >First convert .bed file from narrowpeak file(gz) >Use the blacklist filtered one!!!! ```script=1 gunzip -c /home/stian/outerspace/PEAS_trying/depo/pipeline_outputs/organized_outputs_50K/peak/rep1/SRR891268_1.trim.srt.nodup.no_chrM_MT.tn5.pval0.01.500K.narrowPeak.gz > /home/stian/outerspace/PEAS_trying/depo/footprint/GM50K_rep1 cut -f 1,2,3 GM50K_rep1 >GM50K_rep1.bed ``` ```script=1 TOBIAS ATACorrect --bam /home/stian/outerspace/PEAS_trying/depo/pipeline_outputs/organized_outputs_50K/align/rep1/SRR891268_1.trim.srt.nodup.no_chrM_MT.bam --genome /home/stian/outerspace/PEAS_trying/depo/example_data/hg38.fa --peaks GM50K_rep1.bed ``` ## 2. ScoreBigwig ```script=1 TOBIAS FootprintScores --signal SRR891269_1.trim.srt.nodup.no_chrM_MT_corrected.bw --regions GM50K_rep2.bed --output GM50K_rep2_footprints.bw --cores 8 ``` ## 3. FootprintScores ```script=1 TOBIAS FootprintScores --signal SRR12098205_1.trim.srt.nodup.no_chrM_MT_corrected.bw --regions v2_MM1S_rep1.bed --output v2_MM1S_rep1_footprints.bw --cores 8 ``` output sample: '*.bw'