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HT-seq Counts Stranded option

Hi everyone,

I am having a trouble understanding HT-seq Counts. I have a first strand library (dUTP). This data was previously analyzed incorrectly using the option stranded = Yes by someone else. I have reanalyzed it with Stranded = Reverse which is the correct option. Here is a subset of the count table from one sample:

                        Gene    Stranded = Yes  Stranded = Reverse
          ENSDARG00000000001            7               114
          ENSDARG00000000002            12               37
          ENSDARG00000000018            28             1047
          ENSDARG00000000019            24             1236
          ENSDARG00000000068            8               308 
          ENSDARG00000000069            17             1014
          ENSDARG00000000086            25               88
          ENSDARG00000000103            98             4159
          ENSDARG00000000142            2                98
          ENSDARG00000000151            1                34

Can someone please help me understand how HT-seq count is doing the counting. Why does using stranded =Reverse with the data set produce more read counts than Stranded = Yes. I need to be able to understand the underlying reason why the counts are so different.

Thanks,

rna-seq ht-seq counts gene
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written by Krish Srinivasan • Krish Srinivasan

Hi! Have you found the answer? Thank you!

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written by o.mikh90 • o.mikh90

1 answer

thanks for the reply, but i have looked through those already and it didn't answer my question.

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written by Krish Srinivasan • Krish Srinivasan

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