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Old 01-07-2010, 10:23 AM   #1
chrisbala
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Default bowtie, no .rev files produced

hi everyone,

taking my first crack at index building using bowtie.

I'm trying to build my index using a whole genome assembly in a single fasta file.

i first ran with all defaults, and bowtie produced only 4 files.

Both of the .rev files were not generated.

For now we are not doing paired end reads, so I should probably use the -r (which I haven't done yet). But any thoughts on why I am missing those files?

Chris
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Old 01-07-2010, 10:29 AM   #2
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oops. wait a sec. first silly question by me (not last). index is still being built....
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Old 01-07-2010, 10:34 AM   #3
chrisbala
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sure enough, now I have . rev files...
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Old 01-07-2010, 08:30 PM   #4
Xi Wang
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You just took several mins to build the index, what is your genome size?
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Old 01-08-2010, 06:28 AM   #5
chrisbala
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Default genome size

the genome is about 1Gb.

I made the index using a single fasta file containing the whole genome.

sound ok?
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Old 01-08-2010, 09:05 PM   #6
Xi Wang
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it took several hours to build hg18 index, of which the genome size is ~3Gb. what are your options when running the program? I did not think it matters much whether the input is a single fasta file or several fasta files.
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Old 01-09-2010, 06:46 AM   #7
chrisbala
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Default index, tophat_report

since it was my first try and i had just installed the software, i just used all defaults.

I'm running on a new cluster with 24 GB memory per node, and 2.4 GHz processors.

Right now I'm stuck with this problem if anyone has any suggestions.

[Fri Jan 8 21:33:28 2010] Reporting output tracks
[FAILED]
Error: tophat_reports not found on this system
Traceback (most recent call last):
File "/share/apps/tophat/tophat", line 1518, in ?
sys.exit(main())
File "/share/apps/tophat/tophat", line 1490, in main
params.gff_annotation)
File "/share/apps/tophat/tophat", line 963, in compile_reports
exit(1)
TypeError: 'str' object is not callable
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