<p>If you have a SNP panel then you have the coordinates on the genome. You can use tools such as <a href="https://bedtools.readthedocs.io/en/latest/content/tools/slop.html" rel="nofollow noreferrer">bedtools slop</a> to expand the coordinates to the desired length and then extract those regions from the target genome using <a href="https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html" rel="nofollow noreferrer">bedtools getfasta</a>.</p>

CC BY-SA 4.0
2022-07-01T04:20:54.210Z
Thank you! That's very helpful. The dilemma, however, is we'd like to extract the 300bp sequences from a different genome, and not from the reference genome of the SNP panel, therefore the coordinates on the SNP panel will not be exactly on our genome.
Umi Rayearth
CC BY-SA 4.0
2022-07-01T07:51:28.863Z
Then you need liftover https://genome.ucsc.edu/cgi-bin/hgLiftOver
I don't know if the genomes you're working on have mapping files though.
asafpr
CC BY-SA 4.0
2022-06-29T06:04:41.580Z
2022-06-29T06:04:41.580Z
asafpr
<p>I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.</p>
<p>Anyone knows what bioinformatics tool I can use for this? Thank you!</p>
<p><em>Actual scenario:</em>
The SNP sequences are from a SNP panel data (90bp sequence, SNP is at the middle). We would like to extend the sequence to 300bp, retaining the SNP at the middle so we can make a sequence capture panel of the SNP.</p>

CC BY-SA 4.0
2022-06-29T06:38:19.690Z
You mean the target capture panel of SNP markers?
envs_h_gang_5
CC BY-SA 4.0
2022-06-29T12:41:43.580Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2022-07-01T04:17:30.433Z
@envs_h_gang_5 I'm actually not very familiar, but something like 'genotyping by sequencing' kind of panel.
Umi Rayearth
<phylogenetics><snp><read-mapping>
What tool I can use to map short-reads sequences to reference genome and get specific mapped size
# What tool I can use to map short-reads sequences to reference genome and get specific mapped size

(Asked by: username_0 on 2022-06-29)

I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.

Anyone knows what bioinformatics tool I can use for this? Thank you!

*Actual scenario:*
The SNP sequences are from a SNP panel data (90bp sequence, SNP is at the middle). We would like to extend the sequence to 300bp, retaining the SNP at the middle so we can make a sequence capture panel of the SNP.

**Tags:** phylogenetics, snp, read-mapping
> **Comments:**
> **username_1**: You mean the target capture panel of SNP markers?  
> **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_0**: @envs_h_gang_5 I'm actually not very familiar, but something like 'genotyping by sequencing' kind of panel.  

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## 1 answers

### Answer by username_3 on 2022-06-29. Score: 3

If you have a SNP panel then you have the coordinates on the genome. You can use tools such as [bedtools slop](https://bedtools.readthedocs.io/en/latest/content/tools/slop.html) to expand the coordinates to the desired length and then extract those regions from the target genome using [bedtools getfasta](https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html).

> **Comments:**
> **username_0**: Thank you! That's very helpful. The dilemma, however, is we'd like to extract the 300bp sequences from a different genome, and not from the reference genome of the SNP panel, therefore the coordinates on the SNP panel will not be exactly on our genome.  
> **username_3**: Then you need liftover https://genome.ucsc.edu/cgi-bin/hgLiftOver I don't know if the genomes you're working on have mapping files though.  

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