Question: unalign bam and convert to fastq
0
gravatar for bioguy24
3.9 years ago by
bioguy24190
Chicago
bioguy24190 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 • 1.2k views
ADD COMMENTlink modified 3.9 years ago by thackl2.6k • written 3.9 years ago by bioguy24190
0
gravatar for thackl
3.9 years ago by
thackl2.6k
MIT
thackl2.6k wrote:

Have a look at samtools bam2fq

ADD COMMENTlink written 3.9 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 3.9 years ago by bioguy24190
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 3.9 years ago • written 3.9 years ago by geek_y9.8k
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 3.9 years ago by bioguy24190
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