SciLifeLab/NGI-RNAseq

biotypes chart showing only last 7 entries

Closed this issue · 2 comments

Hi,
is this on purpose? it selects only last seven biotypes from tmp_file , missing protein coding genes and other important groups leaving the chart quite meaningless (at least in my case).

cut -f 1,7 ${bam_featurecounts.baseName}_biotype.featureCounts.txt | tail -n 7 > tmp_file

I'd suggest adding something like
cut -f 1,7 ${bam_featurecounts.baseName}_biotype.featureCounts.txt | sort -k 2 -n -r | head -n 10 > tmp_file

thanks,
JK

ewels commented

Ah no, I guess this was accidental - maybe the file that @Hammarn was looking at only had 7 categories or something?

hmm, I have no idea why I did this. I don't really see a point in restricting the categories at all to be honest. It's not that many.I'll make a PR.