Question: Paired end FASTA to single BAM file
0
gravatar for jyu429
3.3 years ago by
jyu429120
United States
jyu429120 wrote:

Hi,

I'm interested in taking two fastq files X_1.fq and X_2.fq creating a single bam file X.bam, unmapped to anything. Is there a way to do this with just bowtie2 and samtools? Thank you for the help!

samtools • 883 views
ADD COMMENTlink modified 3.3 years ago by igor8.9k • written 3.3 years ago by jyu429120

Just curiously, what are reasons one would do this?

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by datascientist28410
1

I don't know about the original poster, but BAM is actually a more efficient file format. Check this post: http://blastedbio.blogspot.com/2011/10/fastq-must-die-long-live-sambam.html

ADD REPLYlink written 3.3 years ago by igor8.9k
2
gravatar for igor
3.3 years ago by
igor8.9k
United States
igor8.9k wrote:

Would Picard be acceptable? You can do it easily with FastqToSam: https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by igor8.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1625 users visited in the last hour