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Old 09-18-2014, 02:41 AM   #3
LeonDK
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Location: Denmark

Join Date: Sep 2014
Posts: 69
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Quote:
Originally Posted by dpryan View Post
Have a look at the --transcriptome-index option, which is what you're looking for.
Hi dpryan,

Thanks for input reg. the --transcriptome-index option for tophat2. I looked it up in the TopHat2 manual. For other users, which may encounter the same challenge - The trick is to run this command first:
Code:
tophat2 -G iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --transcriptome-index=transcriptome_data/known iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
and then subsequently call tophat2 with this command:
Code:
tophat2 --num-threads 12 --transcriptome-index=transcriptome_data/known iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome myfastq_R1.fastq.gz myfastq_R2.fastq.gz
After running the above command, you'll see
Code:
[2014-09-18 12:12:04] Using pre-built transcriptome data..
Which is significantly faster, when running multiple samples.

The UCSC/hg19 data can retrieved like so:
Code:
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
Cheers,
Leon
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