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Tophat colorspace problem
Hello everyone,
I'm trying to get tophat work with csfasta and qual files.
My command is now:
tophat2 -G ../GENOMES/human_GRCh37_gatk/GRCh37_genes_nochr.gtf -T --bowtie1 -C -r 175 -p 7 -Q --library-type fr-secondstrand ../GENOMES/human_GRCh37_gatk/GRCh37_gatk csfasta/testF3.csfasta,csfasta/testF5.csfasta csfasta/testF3_QV.qual,csfasta/testF5_QV.qual
The output is now an error message:
Error running 'prep_reads'
what(): basic_string::substr
The .csfasta looks like this:
>1_104_494_F5-BC
G3333333223303333031330.3323........
The .qual file looks like this:
>1_104_494_F5-BC
7 6 12 12 17 13 4 5 5 13 7 10 5 7 12 9 5 4 4 5 4 4 -1 7 6 4 4 -1 -1 -1 -1 -1 -1 -1 -1
I installed bowtie version 0.12.8.0
And samtools version 0.1.18.0
Tophat is version 2.0.6
What am I doing wrong?
I'm trying to get tophat work with csfasta and qual files.
My command is now:
tophat2 -G ../GENOMES/human_GRCh37_gatk/GRCh37_genes_nochr.gtf -T --bowtie1 -C -r 175 -p 7 -Q --library-type fr-secondstrand ../GENOMES/human_GRCh37_gatk/GRCh37_gatk csfasta/testF3.csfasta,csfasta/testF5.csfasta csfasta/testF3_QV.qual,csfasta/testF5_QV.qual
The output is now an error message:
Error running 'prep_reads'
what(): basic_string::substr
The .csfasta looks like this:
>1_104_494_F5-BC
G3333333223303333031330.3323........
The .qual file looks like this:
>1_104_494_F5-BC
7 6 12 12 17 13 4 5 5 13 7 10 5 7 12 9 5 4 4 5 4 4 -1 7 6 4 4 -1 -1 -1 -1 -1 -1 -1 -1
I installed bowtie version 0.12.8.0
And samtools version 0.1.18.0
Tophat is version 2.0.6
What am I doing wrong?