EricKutschera
commented
7 months ago This is the code that reads the .rmats files: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_pipeline/rmatspipeline/rmatspipeline.pyx#L3540
- The 1st line is the bam file (or files) that this .rmats file is for
- The 2nd line is the --readLength
- The next line starts the section about novel junction reads. This line is the number of novel junction lines that are in this section
- For each novel junction line the format is
gene_id;start,mid,end;start,mid,end;...- start, mid, and end are each an index of an exon in the gene
- with --novelSS the values can also be negative and represent a novel splice site coordinate
- After the novel junction section the next line says how many lines are in the next section about exon reads
- For each exon line the format is:
gene_id;min_start,max_start,min_end,max_end,count;min_start,max_start,min_end,max_end,count;...- instead of recording each possible read start and end position, the reads are grouped together according to min,max start,end
- rmats chooses which coordinates to use for the min,max values so that it still has enough information to know if the reads covered specific splice sites
- there can also be -1 values here which essentially mean no value
- After the exon read section the next line says how many lines are in the next section about junction reads
- For each junction read line the format is:
gene_id;start:start=splice_site1:splice_site2=splice_site3:splice_site4=...=end:end,count;start:start...- essentially the reads are grouped according to splice sites and then counted
- there can be -1 values here which mean the splice site is novel and rmats will not use that coordinate
Hi,
Could you explain the content of prep .rmats file? I want to do some intermediate summary, like how many reads from the bam were utilized to support the overall AS event. Thanks for your help.