Tag: treat_pileup
1 is not found in chromosome sizes file
1 is not found in chromosome sizes file 0 I am trying to convert bedGraph to bigWig file with bedGraphToBigWig. but I always get “1 is not found in chromosome sizes file”. I used the following script macs2 callpeak -c SRRc_sorted.bam -t SRRe_sorted.bam -B –nomodel –extsize 200 –SPMR -q 0.01…
Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias
bdgcmp(1) Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias SYNOPSIS bdgcmp <-t TREATMENT.BEDGRAPH> <-c CONTROL.BEDGRAPH> <-o OUTPUT.BEDGRAPH> [-m METHOD] DESCRIPTION Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing…
difference between treat_pileup and bdgcmp fold enrichment tracks macs2
difference between treat_pileup and bdgcmp fold enrichment tracks macs2 0 Hello, I created bigwig file from a treat_pileup.bdg file generated by macs2 and also used treat_pileup.bdg and control_lambda.bdg with macs2 bdgcmp. Here is my codes; macs2 callpeak -t sample.bam -c sample_input.bam -g hs -f BAM -q 0.001 –bdg –outdir /folder…
