Bowtie2 long index(.bt21) and tophat

[pengchy]

@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.

[yifeng]

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]

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

[sbdk82]

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

[GenoMax]

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]

I am using tophat2 with long index with suffixes .bt21. But it is giving the following error

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