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Old 05-13-2009, 12:58 AM   #1
arendon
Junior Member
 
Location: Cambridge, UK

Join Date: Mar 2009
Posts: 6
Default Tophat with GRC37

Hey there!

I am trying to use tophat (1.0.7) with the new human genome version GRC37 (aka hg19). I get an error quite late into it:

...
Sat May 9 23:25:26 2009] Mapping reads against hg19 with Bowtie
[Sat May 9 23:55:13 2009] Searching for junctions via coverage islands
[Sun May 10 00:03:52 2009] Searching for junctions via mate-pair closures
[Sun May 10 07:49:28 2009] Retrieving sequences for splices
[Sun May 10 08:53:56 2009] Indexing splices
Error: Reference sequence has more than 2^32-1 characters! Please divide the
reference into batches or chunks of about 3.6 billion characters or less each
and index each independently.
[FAILED]
Error: Splice sequence indexing failed
...

I have a single fasta file with hg19 and have created all the bowtie indexes.

Wondering what is the best way to split the file and how should I name it.

Thanks a lot, and thanks for all the hard work that went into making tophat and bowtie.

a
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Old 05-13-2009, 08:17 AM   #2
Cole Trapnell
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Location: Boston, MA

Join Date: Nov 2008
Posts: 212
Default

Hi,

This is actually a bug in the latest beta (1.0.7). TopHat builds a Bowtie index of possible splice junctions and then aligns the reads back to this splice index to confirm them. The crash occurs because with some types of reads, TopHat can produce an excessive amount of possible junctions, and the Bowtie indexer bails out.

I'll have a fix up in a few days. Sorry for the trouble.

Cole
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