Question: Extract gene sequence from BAM.
gravatar for Pedro Morell
2.0 years ago by
Pedro Morell0 wrote:

Hi, I have several BAM files with different samples of a chromosome and I want to end up with one file for each sample (two if they are paired) including only a certain region of that chromosome in order to study the variance. I've managed to convert the original BAM I'm using as a test into FASTQ, perform the quality asses, that I already knew was correct, and trim the low quality areas on the edges of each sequence, but I don't know how to cut from the whole chromosome to my target gene sequence. 

Any advise?

fastq sequence gene bam • 700 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson23k • written 2.0 years ago by Pedro Morell0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson23k wrote:


Tools in the groups NGS: SAMtools, NGS: Picard, and BEDtools are the most commonly used to manipulate BAM content (before extracting sequence or other operations). Try Slice BAM first for your case. 

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson23k

I've been working with NGS:SAMtools and NGS:Picard. My first step was to pas from BAM to SAM, and then to FASTQ, a format I'm used to use, but I don't know how to get just the region I want to study. I'll try Slice BAM and see.


ADD REPLYlink written 2.0 years ago by Pedro Morell0
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