The RefFlat format on the UCSC website is described to have "Name of gene as it
appears in Genome Browser" in the 1st column, and "Name of gene" in the 2nd
column. So it sounds like both columns should have a gene name; not a
transcript ID. I run PICARD CollectRnaSeqMetrics using the transcript ID in
both columns and got an output. Should I have instead reduced the alternatively
spliced transcripts to genes and make a RefFlat only from the genes? Will the
Metrics be more accurate using the gene-based rather than the transcript-based
RefFlat? Thank you.
________________________________
From: Nils Homer [nho...@broadinstitute.org]
Sent: Tuesday, February 17, 2015 3:44 PM
To: Trakhtenberg, Feliks
Cc: samtools-help@lists.sourceforge.net
Subject: Re: [Samtools-help] 1st & 2nd columns of RefFlat.txt for PICARD's
CollectRnaSeqMetrics
The second column is the transcript ID I believe. The Refflat format is
described here:
http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat<https://urldefense.proofpoint.com/v2/url?u=http-3A__genome.ucsc.edu_goldenPath_gbdDescriptionsOld.html-23RefFlat&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=S2hvo91xGvF036hUCg2uC3-j5AF8y5RAkzrz4329FQrqSSY3linUUsfPH7jTZCGe&m=RZDLSjTky1mLrpnFYfajtGhOwmfOwgAPdBgXPsbRo18&s=rom265uqDfcJANf51Nb6S8mCKPKefKK-3QWJr1ZvvoU&e=>
N
On Tue, Feb 17, 2015 at 3:23 PM, Trakhtenberg, Feliks
<ephraim.trakhtenb...@childrens.harvard.edu<mailto: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<mailto:nho...@broadinstitute.org>]
Sent: Tuesday, February 17, 2015 2:56 PM
To: Trakhtenberg, Feliks
Cc:
samtools-help@lists.sourceforge.net<mailto: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<mailto: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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