Question: RNA-Seq Mapping and bowtie2 indexing
0
gravatar for debitboro
3.1 years ago by
debitboro110
Belgium
debitboro110 wrote:

Hi all,

I have a PE reads from Illumina (for human breast cancer), I want to do the mapping against the reference human genome GRCh37 (downloaded from iGenome). I perform the mapping with Tophat2 without building the bowtie2 indexes (because, the indexe is included in the downloaded genome). The downloaded genome has ~20Go, and the file I want to map ~ 5 Go (for PE, so two file to include in the Tophat2 command). I have read some posts that recommend to build the indexes (even if the indexe is included in the downloaded reference genome). So, my question is to know what the difference to use the pre-made indexes, and to build the own indexes ?

thanks in advance

ADD COMMENTlink written 3.1 years ago by debitboro110
1

I think you are referring to building a "transcriptome" specific index (that uses only the "known" genes that you provide via an annotation file). See the section on "Supplying your own transcript annotation data" on TopHat manual page.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax67k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1230 users visited in the last hour