The second column is the transcript ID I believe. The Refflat format is
described here:
http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
N
On Tue, Feb 17, 2015 at 3:23 PM, Trakhtenberg, Feliks <
ephraim.trakhtenb...@childrens.harvard.edu> wrote:
> Thank you. What about the 2nd column? Does it matter whether it will
> have transcript or gene ID (like the 1st column? Thanks.
> ------------------------------
> *From:* Nils Homer [nho...@broadinstitute.org]
> *Sent:* Tuesday, February 17, 2015 2:56 PM
> *To:* Trakhtenberg, Feliks
> *Cc:* samtools-help@lists.sourceforge.net
> *Subject:* Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for
> PICARD's CollectRnaSeqMetrics
>
> 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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