RNA-seq analysis
I have paired-end FASTQ files. I used HISAT2 for alignment and got a good alignment percentage. Then, I used featurecounts for getting the raw counts for the genes. I excluded the chimeric fragments using -C command, but I see that most of my reads fall under unassigned chimera and very few are assigned. What could be the issue with it?
• 826 views
•
link
updated
by
rfran010 •
•
written
by
sk_24 •
•
written
by
sk_24 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Gene or Exon Counts for DESeq2 in rRNA-Depleted RNA-seq?
written by n@4j •
-
galaxy and RNA seq
written by nmozdoori •
-
RNA-seq assigned alignments
written by Manko47 •
-
RNA-seq analysis
written by sk_24 •
-
Hi-C Pro
written by sk_24 •
-
Counts after using feature counts is low
written by rajdeepboral00 •
-
Feature Counts: low assigned alignments (1.9%) with -s 0: Unstranded option any assigned alignments…
written by francesca.catellani •
-
low Successfully assigned alignments
written by Srujana •
-
featureCounts: 0% successfully assigned fragments on multiple PE .BAM files
written by imesi •
-
featureCounts not recognizing paired-end alignment file.. why?
written by dec986
More info would be useful, such as some example chimeric reads and some numbers to qualify "most" and "very few", but most reads being chimeric sounds strange.
Few reads being assigned may make sense depending how few and the library type.
For chimeric reads, that would be something that happens during alignment though, so would be good to investigate what are those reads.