Question: unalign bam and convert to fastq
0
gravatar for cmccabe
3.6 years ago by
cmccabe180
Chicago
cmccabe180 wrote:
I would like to unalign a bam file that was aligned by TMAP and create a fastq file. I am going to re-align using bowtie2 using an indexed hg19 reference. Thank you :).
bowtie2 • 1.1k views
ADD COMMENTlink modified 3.6 years ago by thackl2.6k • written 3.6 years ago by cmccabe180
0
gravatar for thackl
3.6 years ago by
thackl2.6k
MIT
thackl2.6k wrote:

Have a look at samtools bam2fq

ADD COMMENTlink written 3.6 years ago by thackl2.6k
Is there a tool or script that can unalign a bam file and output the unaligned bam? Thank you :)
ADD REPLYlink written 3.6 years ago by cmccabe180
1

As said, convert the bam to fastq and re-align with whatever tool you are interested in. Keep in mind about Paired-End, soft/hard clipping etc while converting to fastq. 

Or tell what is meant by unaligned bam ? Do you mean to say extract unaligned reads from bam ?

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by geek_y9.3k
Basically our data has indels in it that are not being called. I have a bam file created using TMAP that I am going to convert to a fastq and realign using bowtie2. Next, I will use bwa on this bam. Does that sound like a goodlan or do you recommend something else? Thank you :).
ADD REPLYlink written 3.6 years ago by cmccabe180
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: 1781 users visited in the last hour