Yes, the gene name should be the first column and this will affect the
output. Unfortunately you will need to put the gene name in the first
column for the tool to produce output as expected.
N
On Sun, Feb 15, 2015 at 2:50 PM, Trakhtenberg, Feliks <
ephraim.trakhtenb...@childrens.harvard.edu> wrote:
> Hello,
>
>
> PICARD CollectRnaSeqMetrics requires RefFlat.txt, which I had to generate.
> I have transcript name in both the 1st and the 2nd columns of my
> RefFlat.txt. Would there be a difference in the output if the 1st column
> would have had a gene name instead of the transcript name (while the 2nd
> column would still have the transcript name)? I ask because I have
> alternatively spliced transcripts and due to the format of my original
> inputs I cannot easily generate the 1st column with gene names to address
> my question.
>
>
> Thank you,
> Ephraim
>
>
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