Question: differences between featureCounts and htseq-count
0
gravatar for golany89
10 months ago by
golany890
golany890 wrote:

Hi, I have RNA-seq data (from ribodepleted samples) and i'm trying to map my reads to features using either htseq or featureCounts. The input for both is a bam file (reads were aligned using STAR) and a GTF file from ENSEMBLE. Both assign reads to exons by default.

FeatureCounts reported that ~33% of my reads were assigned to features, however when I'm trying to check how many reads were assigned using htseq, I saw that only 2% of my reads were assigned (There is no report in htseq so I summerized the second column in the results file, without the last 5 rows that contain the "no-feature" and "ambiguous" etc).

What is causing this difference between the two algorithms? Thank you very much!

rna-seq • 541 views
ADD COMMENTlink written 10 months ago by golany890
2

The differences should be very minor between the two tools. If you post the exact commands used, it will be easier to see what causes the differences.

ADD REPLYlink written 10 months ago by igor11k
2

Is it possible you're using the wrong stranded argument in htseq? The vast majority of stranded libraries (e.g. using the Illumina kit) should use --stranded=reverse NOT --stranded=yes

ADD REPLYlink written 10 months ago by colin.kern920

Thank you very much, this solved the problem.

ADD REPLYlink written 10 months ago by golany890
1
gravatar for Arup Ghosh
10 months ago by
Arup Ghosh2.6k
India
Arup Ghosh2.6k wrote:

Comparison Htseq And Feature Count

ADD COMMENTlink modified 10 months ago by ATpoint36k • written 10 months ago by Arup Ghosh2.6k
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