Dear Group,
I have run TopHat 2.0.9 and 2.0.10 for my 75 PE RNA-sequencing data. Totally, I have 8 samples sequenced on each lane on Illumina HiSeq 2000.
My problem is I got accepted_hits.bam results for 5 samples out of 8. For other 3 samples, the .bam files can be only found under "tmp" dir.
Here is the command
$tophat -r 50 --mate-std-dev 70 --keep-tmp --no-coverage-search -o ./tophat_out /Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome sample1_R1.fastq.gz sample1_R2.fastq.gz
Any help would be very appreciated.
Shirley
I have run TopHat 2.0.9 and 2.0.10 for my 75 PE RNA-sequencing data. Totally, I have 8 samples sequenced on each lane on Illumina HiSeq 2000.
My problem is I got accepted_hits.bam results for 5 samples out of 8. For other 3 samples, the .bam files can be only found under "tmp" dir.
Here is the command
$tophat -r 50 --mate-std-dev 70 --keep-tmp --no-coverage-search -o ./tophat_out /Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome sample1_R1.fastq.gz sample1_R2.fastq.gz
Any help would be very appreciated.
Shirley
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