I'm trying to align my rna-seq data to ref genome using tophat. I made bowtie2 index files, and it is in the working dir.
The code I used is :
"source /usr/local/apps/tophat/tophat.csh
cd /gpfs_share/hlibyar/tophat
tophat Am_genome ../trim/IAPV_05h_TTAGGC_L003_R1_001.trimmed.fastq
"
This is my error msg.
[2014-09-11 16:36:03] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-09-11 16:36:03] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 1.0.0.0
[2014-09-11 16:36:03] Checking for Samtools
Samtools version: 0.1.19.0
[2014-09-11 16:36:03] Checking for Bowtie index files
Error: Could not find Bowtie index files (Am_genome.*.ebwt)
It seems like tophat is looking for ebwt files, but my index are *.bt2
Pls help me here! thanks a lot!
The code I used is :
"source /usr/local/apps/tophat/tophat.csh
cd /gpfs_share/hlibyar/tophat
tophat Am_genome ../trim/IAPV_05h_TTAGGC_L003_R1_001.trimmed.fastq
"
This is my error msg.
[2014-09-11 16:36:03] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2014-09-11 16:36:03] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 1.0.0.0
[2014-09-11 16:36:03] Checking for Samtools
Samtools version: 0.1.19.0
[2014-09-11 16:36:03] Checking for Bowtie index files
Error: Could not find Bowtie index files (Am_genome.*.ebwt)
It seems like tophat is looking for ebwt files, but my index are *.bt2
Pls help me here! thanks a lot!
Comment