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Old 11-02-2014, 05:50 PM   #1
linp5
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Location: China

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Default get FPKM for Ensembl Gene IDs

Hi all:

I am trying to run tophat + cufflink to get FPKM values.

my question here is:
how to use Ensembl Gene IDs, instead of the default cufflinks Gene IDs (e.g. CUFF.1), to represent the results ?

my procedure is rather simple:
1. tophat mm9 SRR306857.fastq
2. cufflinks accepted_hits.bam

What kind of reference file I should add to these computation to get FPKM value for Ensembl Gene IDs?

Thanks in advance!
Best,
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Old 11-02-2014, 11:43 PM   #2
dpryan
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Just download the GTF and use the -G option.
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Old 11-03-2014, 05:01 PM   #3
linp5
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Thank you!

I have used the genes.gtf from NCBIM37, which result in 0 FPKM.
I guess that since I have used mm9 in my Tophat, I should also use mm9-based genes.gtf in my cufflinks?
Is that right?

Thanks in advance!
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Old 11-03-2014, 05:14 PM   #4
GenoMax
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Here is the mm9 GTF file from Ensembl: ftp://ftp.ensembl.org/pub/release-60/gtf/mus_musculus/

NCBI37 = mm9 build
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Old 11-03-2014, 05:17 PM   #5
linp5
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Thank you!
I will give a try!
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