featureCounts assigning reads criteria
I know by default, featureCounts does not count multi-mapping reads. My question is, by default, does featureCounts try to assign the following, or automatically categorize as unassigned?
- singletons (i.e., only one mate is mapped for paired-end reads)
- non-properly paired reads (i.e., both mates mapped, but not necessarily properly paired/in proper orientation)
• 735 views
•
link
written
by
xosugarxspicexo •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
featureCounts for paired-end reads
written by xosugarxspicexo •
-
featureCounts fragment count
written by xosugarxspicexo •
-
Understanding MarkDuplicates and featureCounts results
written by xosugarxspicexo •
-
Getting uniquely aligned properly paired reads
written by nadiabeg.comsats •
-
samtools stats result different from samtools flagstat
written by snishtala03 •
-
samtools filter proper paired alignment
written by mynameliuxiang •
-
How to remove singletons in a BAM file using samtools
written by neranjan •
-
featureCounts for paired bam files and dealing with multimapping reads?
written by bioinfo8
-
Samtools flagstat results
written by Gene_MMP8
-
filtering paired end mapped reads form SAM/BAM file
written by Raghav
