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Old 06-16-2010, 03:17 AM   #1
repinementer
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Location: asia

Join Date: Dec 2009
Posts: 80
Default problem with tophat commnd directing bowtie indexes

here is the command I given. I directed bowtie indexes but not working

I downloaded hg18 index from bowtie ftp site and unzipped in index folder of bowtie by creating a sub directory hg18.
Hope I did every thing correct?

Code:
 tophat -r 200 /home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18 SL001_R00089_RHE011_01pgx2_F3.csfasta SL001_R00089_RHE012_01pgx2_F3.csfasta SL001_R00089_RHE013_01pgx2_F3.csfasta SL001_R00089_RHE014_01pgx2_F3.csfasta SL004_R00058_RHE015_01pgx2_F3.csfasta 

[Wed Jun 16 18:12:39 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed Jun 16 18:12:39 2010] Preparing output location ./tophat_out/
[Wed Jun 16 18:12:39 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /home/bogugk/rnaseq/software/bowtie-0.12.5/indexes.*
Traceback (most recent call last):
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1635, in ?
    sys.exit(main())
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 1556, in main
    (ref_fasta, ref_seq_dict) = check_index(bwt_idx_prefix)
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 634, in check_index
    check_bowtie_index(idx_prefix)
  File "/home/bogugk/rnaseq/software/tophat-1.0.13/bin/tophat", line 569, in check_bowtie_index
    exit(1)
TypeError: 'str' object is not callable
FYI: I also exported index path to .bashrc by plaing this command in .bashrc
Code:
export PATH=$PATH:/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes
/hg18
Please let me know any suggestions.
Thanx
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Old 06-16-2010, 03:57 AM   #2
Bio.X2Y
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As far as I know you don't create a subdirectory for each index. just place the 6 hg18 files in the indexes directory.
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Old 06-16-2010, 09:05 AM   #3
john_mu
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"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18"

That is wrong

You should point the the bowtie-base, rather than the directory.

eg. something like

"/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes/hg18/genome"
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