How to convert transcript counts to gene counts in R?
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@dd482574
Last seen 12 months ago
Germany

Dear all,

I have been given to analyse a dataset like this, where I have the counts for each transcript. Since I want to use DESeq I need to find a way to convert the transcript counts to gene counts. The out put comes from HOMER, and I am not sure if tximport in R supports it(?)

# A tidytable: 54,013 × 9
   transcript             chr   start   end strand Length Copies `Annotation/Divergence` counts
   <chr>                  <chr> <int> <int> <chr>   <dbl>  <int>                   <dbl>  <dbl>
 1 transcript:AT1G01010.1 1      3631  5899 +        2268      1                       0      4
 2 transcript:AT1G01020.1 1      6788  9130 -        2342      1                       0     51
 3 transcript:AT1G01020.2 1      6788  8737 -        1949      1                       0     50
 4 transcript:AT1G01020.3 1      6788  9130 -        2342      1                       0     51
 5 transcript:AT1G01020.4 1      6788  9130 -        2342      1                       0     51
 6 transcript:AT1G01020.5 1      6788  9130 -        2342      1                       0     51
 7 transcript:AT1G01020.6 1      6788  8737 -        1949      1                       0     50
 8 transcript:AT1G01030.1 1     11649 13714 -        2065      1                       0     39

Any idea or suggestion is appreciated!
Would it be just enough to sum the transcripts of each in a new column?

DESeq2 tximport • 1.5k views
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ATpoint ★ 4.2k
@atpoint-13662
Last seen 2 days ago
Germany

Homer is not really standard software for RNA-seq afaik. The easiest would be to use something like salmon to quantify your reads and then use tximport as in the manual. Then you can be sure data are processed correctly in terms of how tximport expects them.

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Thank you ATpoint for the direction. This is GROseq data though not RNAseq and reads map to introns as well. So here comes my problem.

  1. Does a transcript fasta file, ( that salmon or kallisto need) of a reference genome, also contains the introns
  2. If not, how can I create one
  3. Then If I create the right index I can use tximport and go ahead
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