[krafiq]

EricHaugen: What's the "bowtie_index_prefix" in the 2nd option you gave me above?

[dpryan]

dpryan: 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?

The source code for bowtie is available on its website here or here.

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.

[dpryan]

EricHaugen: What's the "bowtie_index_prefix" in the 2nd option you gave me above?

It's the prefix for the output index files, so it can be anything you want. Normal examples would be "hg19", "mm9" and "mm10", for human and two mouse genome versions. When bowtie is later invoked to do alignments, this same prefix is given to it so it knows what to align things against.

[krafiq]

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

[dpryan]

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.