SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   problem with tophat commnd directing bowtie indexes (http://seqanswers.com/forums/showthread.php?t=5538)

repinementer 06-16-2010 03:17 AM

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

Bio.X2Y 06-16-2010 03:57 AM

As far as I know you don't create a subdirectory for each index. just place the 6 hg18 files in the indexes directory.

john_mu 06-16-2010 09:05 AM

"/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"


All times are GMT -8. The time now is 07:02 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.