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Read Group line using Bowtie2
Hello all
I am trying to align paired-end sequences using Bowtie2. In the output I need read group line i.e, @RG line in sam file. I tried giving the following syntax
/bowtie2 -p 15 -t -q -x /bowtieindexes/GRCH38 -q -1 /home/Read1 -2 /home/Read2 -S --rg-id ID:flowcellId_SampleId --rg CN:nameofourgroup --rg DT:dateofreadsproduced /home/output.sam
Bowtie gives me a error ERR: bowtie2 exited with value 1
Where am I doing wrong. Please guide me using correct syntax to get the @RG line.
Thanks in advance.
I am trying to align paired-end sequences using Bowtie2. In the output I need read group line i.e, @RG line in sam file. I tried giving the following syntax
/bowtie2 -p 15 -t -q -x /bowtieindexes/GRCH38 -q -1 /home/Read1 -2 /home/Read2 -S --rg-id ID:flowcellId_SampleId --rg CN:nameofourgroup --rg DT:dateofreadsproduced /home/output.sam
Bowtie gives me a error ERR: bowtie2 exited with value 1
Where am I doing wrong. Please guide me using correct syntax to get the @RG line.
Thanks in advance.