Hello All
I managed to run bowtie2 on pair reads and can get the overall alignment rate in the output.
However since I am using an R script to do it, I would like to extract this "overall alignment rate" directly from bowtie2 and put it in a table.
Is there anyway using the parameters in bowtie to do this so that it only outputs the
"0.55%" (just the "overall alignment rate")
I am using
bowtie2 -x index -p 4 -1 pair.file1_R1_001.fastq -2 pair.file2_R2_001.fastq --no-unal -S file_index.sam
Regards
Andaleef
I managed to run bowtie2 on pair reads and can get the overall alignment rate in the output.
However since I am using an R script to do it, I would like to extract this "overall alignment rate" directly from bowtie2 and put it in a table.
Is there anyway using the parameters in bowtie to do this so that it only outputs the
"0.55%" (just the "overall alignment rate")
I am using
bowtie2 -x index -p 4 -1 pair.file1_R1_001.fastq -2 pair.file2_R2_001.fastq --no-unal -S file_index.sam
Regards
Andaleef