These are chat archives for nellore/rail

9th
Jan 2018
abhinav
@nellore
Jan 09 17:45
@cliu72 hey! which additional summary statistics do you want? counts.tsv.gz already provides the numbers of mapped and unmapped reads in each sample
it also tells you how many reads are mapped uniquely
and you can subtract that from the total number of mapped reads to obtain the number of multimappers
Candace Liu
@cliu72
Jan 09 22:42
Hi! Thanks for such a quick response. Yeah, I realize I can calculate summary statistics manually, but was just wondering if they were readily available in some sort of final log file (like in STAR). MutliQC tries to avoid calculating these statistics because it slows down the generation of the HTML report.
abhinav
@nellore
Jan 09 22:43
hey, yeah
so what i'm confused about is counts.tsv.gz is telling you exactly the summary statistics
which additional ones do you want?
one could also write multimapped reads, yes, but if you want them right now you can perform the subtraction between two columns of counts.tsv.gz: something like gzip -cd counts.tsv.gz | tail -n +2 | rev | cut -f1 | rev | awk -F',' '{print $1-$2}' will give you the number of multimappers