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-   -   Bowtie2 long index(.bt21) and tophat (http://seqanswers.com/forums/showthread.php?t=44980)

sbdk82 07-15-2014 03:59 PM

Bowtie2 long index(.bt21) and tophat
 
I am using tophat2 with long index with suffixes .bt21. But it is giving the following error

HTML Code:

Could not find Bowtie 2 index files (.*.bt2)

GenoMax 07-15-2014 05:21 PM

As of TopHat v.2.0.11 64-bit bowtie2 indexes were not supported. A new maintenance release is out (v. 2.0.12) but it is likely that long indexes are still not supported.

sbdk82 07-15-2014 06:21 PM

Yes, I am using tophat/2.0.12 but still getting that error. Anyway, thanks for your reply.

pengchy 11-14-2014 11:35 PM

try to change "bt2" into "bt2l" in the tophat source file.

yifeng 08-28-2015 07:40 AM

Quote:

Originally Posted by pengchy (Post 154783)
try to change "bt2" into "bt2l" in the tophat source file.

@pengchy: Will this work by changing bt2 to bt2l in source?

I am using tophat 2.1.0, still have problem of using bt2l. Any solutions so far? I am working on a very genome, so have to use bt2l. Can I align each chromosome separately, and then merge the bam files?

pengchy 09-04-2015 06:32 AM

Quote:

Originally Posted by yifeng (Post 179803)
@pengchy: Will this work by changing bt2 to bt2l in source?

I am using tophat 2.1.0, still have problem of using bt2l. Any solutions so far? I am working on a very genome, so have to use bt2l. Can I align each chromosome separately, and then merge the bam files?

Yes, I have tested this on tophat-2.0.13.Linux_x86_64/tophat successfully.


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