Hi, I was trying to use Tophat2 to align fastq data to mm9 genome. after trimming to get rid of the adaptors, i used command:
tophat2 -p 30 --GTF ~/Ref_sequence/mm9_genes.gtf ~/Tool/bowtie2-2.2.9/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/Bowtie2Index filename.cut4.fastq &
to in order to get mapping done.
One issue is that the pipe would get broken before the job finishes. Since I used the “&” at the end of my command, so I thought the command will be carried out, anyway. but when I checked the outputs, it seems that the command was not carried out until the end.
So do I need to do something to prevent the pipe from broken to keep the command running?
Or once I put the command in the background by ampersand sign “&”, I do not have to worry about it. the issue was caused by other things?
Do anyone has any suggestions?