Question: counting the reads mapped only to the coding sequence
0
gravatar for alirezamomeni707
2.3 years ago by
alirezamomeni7070 wrote:

I have aligned the RNAseq data to the transcriptome and have .bam files. now I want to count the reads that map to the coding sequence not the whole transcriptome. I usually use HTseq count to do so. do you guys know how to do that?

rna-seq • 654 views
ADD COMMENTlink modified 2.3 years ago by h.mon28k • written 2.3 years ago by alirezamomeni7070

I usually use HTseq count to do so.

So what's the problem then? Seems you already know the solution.

ADD REPLYlink written 2.3 years ago by WouterDeCoster42k
1
gravatar for VHahaut
2.3 years ago by
VHahaut1.1k
Belgium
VHahaut1.1k wrote:

Did you look at this answer?

Question: htseq counts on genes (introns + exons)

ADD COMMENTlink written 2.3 years ago by VHahaut1.1k
1
gravatar for h.mon
2.3 years ago by
h.mon28k
Brazil
h.mon28k wrote:

Why don't you tell exactly what you did - commands included?

Usually, when reads are aligned to a transcriptome, one uses RSEM or eXpress (or some other expectation-maximization algorithm) to perform quantification of transcript expression.

Now, in case you aligned to the genome and have a gene annotation, you can use HTSeq or (better) featureCounts to perform quantification of gene expression.

ADD COMMENTlink written 2.3 years ago by h.mon28k
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