Homo_sapiens. GRCh37.55.gtf for tophat

[shouguogao]

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 http://seqanswers.com/forums/showthread.php?t=8247
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?

[Jon_Keats]

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.

[shouguogao]

Thanks for your reply

I did use bowtie index in Ensembl GRCh37 from http://tophat.cbcb.umd.edu/igenomes.html 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.