Tophat - Could not find Bowtie 2 index files

[janaahan13]

Hi,

This is my first RNA seq experience. I tried running tophat2 using

tophat2 –GTF home/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --library-type fr-unstranded --mate-inner-dist 100 –numthreads 1 --output-dir Sample86103_output home/iGenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/ Sample_86103_R1.fastq Sample_86103_R2.fastq

I get this error

[2012-11-27 17:15:34] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-11-27 17:15:34] Checking for Samtools
Samtools version: 0.1.18.0
[2012-11-27 17:15:34] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (GTF.*.bt2)

But my ls shows me all the indices

ls home/iGenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.fa genome.rev.1.bt2 genome.rev.2.bt2

How can I solve this?

[westerman]

1) Use double-dashes for '--GTF' ... Be aware of the times when a double-dash is needed and when a single-dash will suffice.

2) Give the name of your bowtie index; e.g., home/iGenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome

I am not 100% sure of the latter suggestion. The first suggestion is required and actually shows up in your error message.

[janaahan13]

The second suggestion worked.. Thanks westerman