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Old 06-30-2015, 05:07 AM   #3
imsharmanitin
Postdoc Cancer Bioinformatics
 
Location: Olso, Norway

Join Date: Dec 2014
Posts: 17
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Quote:
Originally Posted by GenoMax View Post
Tophat2 uses the entire human genome index files and then creates a "transcriptome-only" subset using information in the GTF file. You only need to do this once, as you discovered.

so this will be the workflow:

1) generate whole genome index using bowtie2
Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
Homo_sapiens.GRCh37.75.gtf


2) the using tophat 2 to create a "transcriptome-only" subset using the whole genome index flie created in step 1

3) point the tophat 2 to the directory containing "transcriptome-only" subset using

--transcriptome-index <directory containing "transcriptome-only" subset>

for subsequent runs
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