I did run tophat-2.1.0.OSX_x86_64 with a command line.
tophat2 –p 4 –G /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2014-05-23-16-05-10/Genes/genes.gtf –o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs --library-type=fr-unstranded --no-novel-juncs /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_1.fastq /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_2.fastq
But, I had an error at below.
[2015-09-25 17:15:17] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:15:17] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-09-25 17:15:17] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)
So, firstly I checked the 'PATH' of the index files. But there was no problem.
/Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/
And then, I confirmed the .*.bt2 files downloaded from iGenomes in the 'PATH'. But those were also fine.
-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.2.bt2
-rwxr-xr-x@ 1 Taehyuk staff 4715 May 23 2012 genome.3.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884433 May 23 2012 genome.4.bt2
lrwxr-xr-x@ 1 Taehyuk staff 29 Jun 14 2012 genome.fa -> ../WholeGenomeFasta/genome.fa
-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.rev.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.rev.2.bt2
I did try to use the most recent bowtie2 (2.2.6). But the result was the same.
[2015-09-25 17:23:42] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:23:42] Checking for Bowtie
Bowtie version: 2.2.6.0
[2015-09-25 17:23:42] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)
I also tried to replace the index files with those from Bowtie2 site (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), but I couldn't fix it.
I have read several threads in this forum to solve this issue, but I couldn't find a suitable solution. Could you give me any suggestions to figure out this issue please? Many thanks!
taehee
tophat2 –p 4 –G /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2014-05-23-16-05-10/Genes/genes.gtf –o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs --library-type=fr-unstranded --no-novel-juncs /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_1.fastq /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_2.fastq
But, I had an error at below.
[2015-09-25 17:15:17] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:15:17] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-09-25 17:15:17] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)
So, firstly I checked the 'PATH' of the index files. But there was no problem.
/Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/
And then, I confirmed the .*.bt2 files downloaded from iGenomes in the 'PATH'. But those were also fine.
-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.2.bt2
-rwxr-xr-x@ 1 Taehyuk staff 4715 May 23 2012 genome.3.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884433 May 23 2012 genome.4.bt2
lrwxr-xr-x@ 1 Taehyuk staff 29 Jun 14 2012 genome.fa -> ../WholeGenomeFasta/genome.fa
-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.rev.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.rev.2.bt2
I did try to use the most recent bowtie2 (2.2.6). But the result was the same.
[2015-09-25 17:23:42] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:23:42] Checking for Bowtie
Bowtie version: 2.2.6.0
[2015-09-25 17:23:42] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)
I also tried to replace the index files with those from Bowtie2 site (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), but I couldn't fix it.
I have read several threads in this forum to solve this issue, but I couldn't find a suitable solution. Could you give me any suggestions to figure out this issue please? Many thanks!
taehee
Comment