Question: RNA-seq data to check impact of PCR duplicates
gravatar for hasanul101
7 months ago by
hasanul1010 wrote:

I have aligned my reads using HISAT, filtered and merged my data into a BAM file. I have tried reading counts using HT-seq but failed to get any results. What other tools should i use to read counts for my data(RNA-seq,PE)? My data is required for differential gene expression(DESeq)

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by hasanul1010
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


FeatureCounts is an alternative tool. Example usage is in the tutorials linked below.

However, getting no results from HTseq-count usually means there is a problem with the reference annotation and if present, can impact FeatureCounts results as well.

  • Verify the content and format. GFF/GTF formatted data is accepted, GFF3 is not. Use the tool gffread to convert, if needed.
  • Also check to make sure the reference annotation is an exact match for the genome build/source used for mapping, Mismatches will effectively result in the annotation not actually being used when counting up the input BAM's mapped reads.

Galaxy support FAQs:

Galaxy Tutorials, including those for RNA-seq:

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson25k
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