Question: How to extract a region from a reference sequence which does not align with a given query read?
0
gravatar for pradyumna Sagar
17 months ago by
Manipal, School Of Life Sciences
pradyumna Sagar20 wrote:

I have a query sequence with 1935 bp and a reference sequence with 2817 bp. My query aligns fully with the reference sequence. I need to extract the regions from the reference sequence(2817bp) which are not a part of my query i.e.approximately 882 bp. I need to do this for many such files (nearly 200). Please help me with a script if possible. I couldn't find any tools online for the same. Kindly help!

ADD COMMENTlink modified 24 days ago by Snijesh VP180 • written 17 months ago by pradyumna Sagar20
2

Look at the samtools faidx solution: Extract User Defined Region From An Fasta File

ADD REPLYlink written 17 months ago by genomax34k

what if i do not know the coordinate regions? I mean as I have mentioned I have to perform this nearly 200 times so it will be difficult to check the coordinates of the reference file which do not match with my query each time. Can you help me with a solution which will directly extract the unaligned region from the reference from a SAM/BAM file?

ADD REPLYlink written 17 months ago by pradyumna Sagar20
1

extract the region with 0 coverage bedtools: extracting no coverage regions

ADD REPLYlink written 17 months ago by Pierre Lindenbaum99k

Can you please explain in detail? I am a beginner.

ADD REPLYlink written 17 months ago by pradyumna Sagar20

The link that Pierre provided gives the exact command. What additional explanation do you require?

ADD REPLYlink written 17 months ago by harold.smith.tarheel3.8k
1
gravatar for Snijesh VP
24 days ago by
Snijesh VP180
India
Snijesh VP180 wrote:

Try the following

samtools faidx reference.fasta

samtools faidx reference.fasta chr:1-n
ADD COMMENTlink modified 24 days ago • written 24 days ago by Snijesh VP180
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