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

Question

[kamel]

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

Answer 1

[achits]

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

[kamel]

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

Answer 2

[Matina]

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

Answer 3

[swbarnes2]

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.