Question: The discrepancy between FeatureCount output and what appeared on the IGV viewer
0
gravatar for cll710426
15 days ago by
cll7104260
cll7104260 wrote:

I am analyzing small RNA-seq data. I mapped the reads with BWA and used FeatureCounts to count reads mapped to individual microRNAs and found the following issues.

For microRNA genes with uniquely mapped reads (Primary @ MAPQ 25, X0=1, XT=U),

1)When I used only -M option, it gives a read count = 1 per uniquely mapped read. However, when I use --fraction -M option, it gives a read count = 0.25 or 0.33 or 0.5 per uniquely mapped read. Isn't it true that FeatureCount should only assign a fraction for a multimapping read but not a uniquely mapped read? This happened in almost all genes.

2) When I did not use -M option, it gives a read count = 0 per uniquely read. FeatureCount gives a lot of zero count per feature when there are uniquely mapped reads (Primary @ MAPQ 25, X0=1, XT=U).

I am not sure how to troubleshoot and am looking for advice from the community. Thank you.

rna-seq featurecount • 96 views
ADD COMMENTlink modified 11 days ago • written 15 days ago by cll7104260
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 858 users visited in the last hour