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Question: Extract gene sequence from BAM.
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gravatar for Pedro Morell
2.9 years ago by
Pedro Morell • 0
Elche
Pedro Morell • 0 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 • 1.2k views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by Pedro Morell • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

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.

Thanks.

ADD REPLY • link written 2.9 years ago by Pedro Morell • 0
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