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Question about which option should I choose (reversely stranded or forward stranded)

Hi,

I have single end data mRNA sequenced by TruSeq stranded mRNA library prep Kit. For quantization i need to know if are reversely stranded or forward stranded.

Do you have an idea which option should I choose?

Thank you in advance

rna-seq sequencing counts
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updated by swbarnes2 swbarnes2 • written by kamel • kamel

3 answers

This was similarly answered in this thread htseq-count: -s reverse vs -s stranded

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written by achits • achits

I saw this thread but I did not really understand. I know if diractemebt from this kit that I used I will be able to know which option to choose

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written by kamel • kamel

Hi Kamel,

Your data might be reversely stranded but I think you need to investigate more and also check with the facility that did the sequencing. You can use infer_experiment.py program from the ResQC package to "guess" the directionality of your data. You can alternatively visualise your data with IGV. A couple more useful resources are the following:

  1. Directional RNA-seq data which parameters to choose? (Chipster manual)
  2. Table S5 from Malachi Griffith et al.

Hope this helps,

Matina

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written by Matina Matina

Why don't you just try each, and see what happens? One should look terrible, and one should look fine. That's likely faster than waiting for someone to spoon-feed you the answer here.

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written by swbarnes2 swbarnes2

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