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Old 09-04-2010, 12:50 PM   #1
joseph
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Default maximum number of the reference input files for bowtie-build

Hi
Is there a maximum number of the reference input files for bowtie-build?
I am trying to build a Bowtie index from a set of 500 DNA sequences; I get the following error:
Code:
Error: could not open seq_x.fa
When I remove seq_x.fa and all the seq_*.fa after it, bowtie-build works fine.
What do you do when you have a high number of reference input files?
I am using Bowtie 0.12.5.
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Old 09-04-2010, 01:13 PM   #2
john_mu
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using "seq_*.fa" won't work with bowtie-build, the output won't be all your sequence files.

If you want to input a list you need to separate each file with commas.

I'm not sure why it fails with your FASTA file, you'll have to wait for Ben Langmead to reply.
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Old 09-04-2010, 02:09 PM   #3
joseph
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Quote:
Originally Posted by john_mu View Post
using "seq_*.fa" won't work with bowtie-build, the output won't be all your sequence files.

If you want to input a list you need to separate each file with commas.

I'm not sure why it fails with your FASTA file, you'll have to wait for Ben Langmead to reply.
I used files separated with commas:

Code:
bowtie-build -f seq1.fa,seq2.fa,...,seqn.fa my_ebwt_base
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