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Old 07-26-2012, 02:38 PM   #1
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Location: USA

Join Date: Jul 2012
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Default How to extract the "overall alignment rate" from bowtie

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


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