Bowtie2

Question

[Sudeep]

Hi everyone, I am using bowtie2 for aligning my chip-seq data. Is there a way to get output as bam file (instead of sam and then converting into bam) and log file? Thank you in advance!! -Sudeep

Answer 1

[Alex]

From bowtie2 manual for the log:

--met-stderr <path> Write bowtie2 metrics to the "standard error" ("stderr") filehandle. This is not mutually exclusive with --met-file. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: --met. Default: metrics disabled.

And just pipe the output to samtools, eg:

bowtie2 --met-stderr metrics.txt -q -x index -1 r1.fastq.gz -2 r2.fastq.gz | samtools sort -o sorted.bam

[Sudeep]

Thank you!!