EricHaugen: What's the "bowtie_index_prefix" in the 2nd option you gave me above?
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Originally posted by krafiq View Postdpryan: I'm sorry-could you please clarify a bit as to what exactly I should do?
Also, is there a way to get the source code for bowtie?
Regarding the remainder, enumerateUniquelyMappableSpace is just a perl script that executes a few other commands, some of which won't work for you because of how the script is structured. I already deleted the Hotspot code (I don't use it) so I can't immediately give you exact changes, but the gist is that you can just edit the code to have bowtie-build index genome.fa rather than a too-long list of scaffold.fa files. There may be a few other lines that will throw errors for similar reasons and you can likely use the same strategy. This all assumes that you know enough to edit a bit of code, of course.
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Originally posted by krafiq View PostEricHaugen: What's the "bowtie_index_prefix" in the 2nd option you gave me above?
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I just tried building a bowtie index using the genome.fa file (without splitting it) and it gave me 4 .ebwt files. And then I used the script:
./enumerateUniquelyMappableSpace.pl 50 Genome | sort-bed - | bedops -m - > Genome.50.mappable_only.bed
but it gave the following error:
Failed to read 50
Warning: Could not find any reads in "-"
# reads processed: 0
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
No alignments
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It's difficult to diagnose your problem when you use multiple pipes. Just run the enumerate command and save that to a file, then try the subsequent commands one at a time and then post which didn't work (probably sort-bed or bedops) and some of the input you're giving it.
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