A bash question

A bash question

0

Hi, I have a set of human exome data sequenced with Agilent Sureselect XT HS2. I am following the Best practice document
www.agilent.com/cs/library/software/public/AGeNTBestPractices.pdf

On p.3 the example for bwa, just want to check if this is correct before starting the long process for alignment.
especially the " at the end and the - after samtools view -b

bwa mem ‐C ‐t 2 /hg38.fa trimmed_dir/sample_R1.cut.fastq.gz   trimmed_dir/sample_R2.cut.fastq.gz | samtools view ‐b ‐ >   aligned_dir/sample.bam"

Any advice would be appreciated! Thanks


bash

• 17 views

updated 1 hour ago by

108k

written 2 hours ago by

▴

20


Login
before adding your answer.

Traffic: 1703 users visited in the last hour

Read more here: Source link