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Old 07-15-2014, 03:59 PM   #1
sbdk82
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Default Bowtie2 long index(.bt21) and tophat

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

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Could not find Bowtie 2 index files (.*.bt2)
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Old 07-15-2014, 05:21 PM   #2
GenoMax
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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.
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Old 07-15-2014, 06:21 PM   #3
sbdk82
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Yes, I am using tophat/2.0.12 but still getting that error. Anyway, thanks for your reply.
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Old 11-14-2014, 11:35 PM   #4
pengchy
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try to change "bt2" into "bt2l" in the tophat source file.
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Old 08-28-2015, 07:40 AM   #5
yifeng
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Quote:
Originally Posted by pengchy View Post
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?
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Old 09-04-2015, 06:32 AM   #6
pengchy
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Quote:
Originally Posted by yifeng View Post
@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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