Hi All,
I met a problem when running Tophat. I just copy tophat, bowtie and cufflinks Unix executable file into local/bin file (I use Mac 10.5). Then I put the prebuilt M. musculus, UCSC mm9 index in the data file, but when I run tophat, could not find bowtie index.
I must have made mistakes, can someone give me some hints.
Thanks in advance!
wei
053:~ wei$ cd /usr/local/bin
053:bin wei$ ls
bed_to_juncs closure_juncs juncs_db tophat_reports
bowtie contig_to_chr_coords library_stats tophat~
bowtie-build cuffcompare long_spanning_reads vpn_uninstall
bowtie-build-debug cufflinks mask_sam vpnclient
bowtie-debug extract_reads prep_reads wish8.5
bowtie-inspect fix_map_ordering segment_juncs
bowtie-inspect-debug gff_juncs tclsh8.5
cisco_cert_mgr ipseclog tophat
053:bin wei$ cd
053:~ wei$ cd desktop/seq/data
053:data wei$ ls -l
total 31530120
-rwxr-xr-x 1 wei staff 1342932855 Jan 8 17:39 42YAVAAX_051109BIC_BasOrth_s_6_sequence.rar
-rwxr-xr-x 1 wei staff 1358512988 Jan 8 17:28 42YAVAAX_051109Ctrl_BasOrth_s_5_sequence.rar
-rwxrwxrwx 1 wei staff 3937882178 Dec 18 14:19 Bic.txt
-rw-r--r-- 1 wei staff 1385985820 Jan 26 19:34 Bic.txt.zip
-rwxrwxrwx 1 wei staff 3966044812 Dec 18 14:19 control.txt
-rw-r--r-- 1 wei staff 1402339205 Jan 26 19:33 control.txt.zip
-rw-r--r-- 1 wei staff 1902 Nov 13 20:56 make_mm9.sh
-rw-r--r--@ 1 wei staff 735209933 Nov 13 16:57 mm9.1.ebwt
-rw-r--r--@ 1 wei staff 319815728 Nov 13 16:57 mm9.2.ebwt
-rw-r--r--@ 1 wei staff 5858 Nov 13 14:35 mm9.3.ebwt
-rw-r--r--@ 1 wei staff 639631445 Nov 13 14:35 mm9.4.ebwt
-rw-r--r--@ 1 wei staff 735209933 Nov 13 19:20 mm9.rev.1.ebwt
-rw-r--r--@ 1 wei staff 319815728 Nov 13 19:20 mm9.rev.2.ebwt
drwxr-xr-x 4 wei staff 136 Jan 27 11:37 tophat_out
053:data wei$ tophat ../../seq/data bic.txt
[Wed Jan 27 11:49:28 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Jan 27 11:49:28 2010] Preparing output location ./tophat_out/
[Wed Jan 27 11:49:28 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files ../../seq/data.*
053:data wei$
I met a problem when running Tophat. I just copy tophat, bowtie and cufflinks Unix executable file into local/bin file (I use Mac 10.5). Then I put the prebuilt M. musculus, UCSC mm9 index in the data file, but when I run tophat, could not find bowtie index.
I must have made mistakes, can someone give me some hints.
Thanks in advance!
wei
053:~ wei$ cd /usr/local/bin
053:bin wei$ ls
bed_to_juncs closure_juncs juncs_db tophat_reports
bowtie contig_to_chr_coords library_stats tophat~
bowtie-build cuffcompare long_spanning_reads vpn_uninstall
bowtie-build-debug cufflinks mask_sam vpnclient
bowtie-debug extract_reads prep_reads wish8.5
bowtie-inspect fix_map_ordering segment_juncs
bowtie-inspect-debug gff_juncs tclsh8.5
cisco_cert_mgr ipseclog tophat
053:bin wei$ cd
053:~ wei$ cd desktop/seq/data
053:data wei$ ls -l
total 31530120
-rwxr-xr-x 1 wei staff 1342932855 Jan 8 17:39 42YAVAAX_051109BIC_BasOrth_s_6_sequence.rar
-rwxr-xr-x 1 wei staff 1358512988 Jan 8 17:28 42YAVAAX_051109Ctrl_BasOrth_s_5_sequence.rar
-rwxrwxrwx 1 wei staff 3937882178 Dec 18 14:19 Bic.txt
-rw-r--r-- 1 wei staff 1385985820 Jan 26 19:34 Bic.txt.zip
-rwxrwxrwx 1 wei staff 3966044812 Dec 18 14:19 control.txt
-rw-r--r-- 1 wei staff 1402339205 Jan 26 19:33 control.txt.zip
-rw-r--r-- 1 wei staff 1902 Nov 13 20:56 make_mm9.sh
-rw-r--r--@ 1 wei staff 735209933 Nov 13 16:57 mm9.1.ebwt
-rw-r--r--@ 1 wei staff 319815728 Nov 13 16:57 mm9.2.ebwt
-rw-r--r--@ 1 wei staff 5858 Nov 13 14:35 mm9.3.ebwt
-rw-r--r--@ 1 wei staff 639631445 Nov 13 14:35 mm9.4.ebwt
-rw-r--r--@ 1 wei staff 735209933 Nov 13 19:20 mm9.rev.1.ebwt
-rw-r--r--@ 1 wei staff 319815728 Nov 13 19:20 mm9.rev.2.ebwt
drwxr-xr-x 4 wei staff 136 Jan 27 11:37 tophat_out
053:data wei$ tophat ../../seq/data bic.txt
[Wed Jan 27 11:49:28 2010] Beginning TopHat run (v1.0.11)
-----------------------------------------------
[Wed Jan 27 11:49:28 2010] Preparing output location ./tophat_out/
[Wed Jan 27 11:49:28 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files ../../seq/data.*
053:data wei$
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