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?
FYI: I also exported index path to .bashrc by plaing this command in .bashrc
Please let me know any suggestions.
Thanx
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:
[B] 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 [/B] [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
Code:
export PATH=$PATH:/home/bogugk/rnaseq/software/bowtie-0.12.5/indexes /hg18
Thanx
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