Hi,
I am using Tophat2 on the grid and trying to get single and paired read unmapped bam files by a following command;
tophat2 -p 16 -o 4560_output -G ~/GRCh37_73.gtf ~/Bowtie2Index2/Ensemble 4650_R1merged.fastq 4650_R2merged.fastq --b2-un-conc ~/4560_output/pefailed.bam --b2-un ~/4560_output/singlefailed.bam
But I only get unmapped.bam but not pefailed.bam and singlefailed.bam. I really appreciate any help with this.
Thanks in advance.
I am using Tophat2 on the grid and trying to get single and paired read unmapped bam files by a following command;
tophat2 -p 16 -o 4560_output -G ~/GRCh37_73.gtf ~/Bowtie2Index2/Ensemble 4650_R1merged.fastq 4650_R2merged.fastq --b2-un-conc ~/4560_output/pefailed.bam --b2-un ~/4560_output/singlefailed.bam
But I only get unmapped.bam but not pefailed.bam and singlefailed.bam. I really appreciate any help with this.
Thanks in advance.
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