Question: How do I get +/- strand orientation info from my RNAseq run?
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3 months ago by
Qiagen Sciences - Frederick Maryland
daniel.kim30 wrote:

I made a RNAseq library using a stranded-RNAseq-library prep kit. The kit only amplifies the transcript strand. I then aligned the paired-end fastq's using HISAT2 using the option for "stranded" and FR (forward read). Typically I use featureCounts to count the genes but I now need strand orientation info in my featureCounts table.

My question is how do I get strand info?


ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by daniel.kim30
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Set these two parameters:

  • Options for pair-end reads, specify the orientation with the parameter Orientation of the two read from the same pair.

  • Advanced Options, specify that the input is stranded with the parameter Strand specificity of the protocol.

The tool form format has changed slightly since this Galaxy tutorial was created, but the methods/options described are still valid:

All tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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