Hi,
I am interested in extracting the unmapped reads. I am using is unparied reads.
Here is the command I use.
bowtie2 -p 8 --no-head --no-unal -x /home/index/allothrnaut -U /home/Fastaqfiles/XGTS.fastq --un /home/Results/unm_xgts.fa --al /home/Results/mp_xgts.fa
But the output of the unmapped reads unm_xgts.fa just remains 0 kb. The unmapped reads are not written to the file.
Am I missing some thing?
Kindly let me know.
Regards
Vishwesh
I am interested in extracting the unmapped reads. I am using is unparied reads.
Here is the command I use.
bowtie2 -p 8 --no-head --no-unal -x /home/index/allothrnaut -U /home/Fastaqfiles/XGTS.fastq --un /home/Results/unm_xgts.fa --al /home/Results/mp_xgts.fa
But the output of the unmapped reads unm_xgts.fa just remains 0 kb. The unmapped reads are not written to the file.
Am I missing some thing?
Kindly let me know.
Regards
Vishwesh
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