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?
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?
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