Question: Single end RNAseq data strandedness infer-experiment-py
0
gravatar for nilus1432
15 months ago by
nilus143230
Singapore
nilus143230 wrote:

Hi all,

I have a single end RNAseq data and would like to understand the strandedness of the data.

  1. From wet-lab input I know "Stranded cDNA library was generated by reverse transcribing the RNA molecules".

  2. I used infer-experiment-py The output is:

This is SingleEnd Data
Fraction of reads failed to determine: 0.0795
Fraction of reads explained by "++,--": 0.0703
Fraction of reads explained by "+-,-+": 0.8502
  

So it's stranded but is it forward or reverse? I do not understand the help given here:

Does it means that its reverse stranded and I have to use s -2 option in featureCounts, "reverse" strandedness in htseq, --rf in StringTie?

Thank you

rna-seq • 611 views
ADD COMMENTlink modified 15 months ago by h.mon29k • written 15 months ago by nilus143230
1
gravatar for h.mon
15 months ago by
h.mon29k
Brazil
h.mon29k wrote:

The majority (85%) of your reads falls in the case described by:

+-,-+
read mapped to ‘+’ strand indicates parental gene on ‘-‘ strand
read mapped to ‘-‘ strand indicates parental gene on ‘+’ strand
  

So yes, your library is reverse stranded. As featureCounts is very fast, you can quickly confirm this by running it with both settings (-s 1 and -s 2), the correct setting will have a much lower count for NoFeature than the incorrect one.

ADD COMMENTlink written 15 months ago by h.mon29k
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