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Old 12-15-2011, 06:18 PM   #1
Junior Member
Location: birminghal al

Join Date: Dec 2011
Posts: 2
Default Homo_sapiens. GRCh37.55.gtf for tophat

I tried to use tophat to generate input files for Altanalyzer

After downloading GRCh37.55.gtf from ensembl, I run

./tophat --GTF Homo_sapiens.GRCh37.55.gtf --output-dir /home/user/tophat_data/NP902 hg19 /home/user/hESC-NP/SRS011902-NP.fq

I got the error message:

Error: reading .... Homo_sapiens.GRCh37.55.gtf .

I tried to follow suggestions in this link
But they do not work for my task.

Homo_sapiens.GRCh37.56.gtf and Homo_sapiens.GRCh37.65.gtf do not work either.

Any suggestions?
shouguogao is offline   Reply With Quote
Old 12-15-2011, 08:20 PM   #2
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

You can't use the hg19 reference genome and ensembl annotations as the chromosomes names don't match (ie. chromosome 1, hg19 = chr1 while ensemble = 1). You can get all the needed files from iGenomes as suggested on the tophat website or create your own bowtie index from the ensemble reference genome file.
Jon_Keats is offline   Reply With Quote
Old 12-16-2011, 02:51 AM   #3
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Location: birminghal al

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Thanks for your reply

I did use bowtie index in Ensembl GRCh37 from as reference genome. I just rename it to hg19. sorry for confusing.
will try to download dna sequence from ensembl and build my own reference genome.
shouguogao is offline   Reply With Quote

error, grch37.55.gtf, tophat

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