User: paulotyama

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paulotyama0
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Posts by paulotyama

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Comment: C: Which SNPs fall within genes and what's their description?
... Thank you @Petr! I used Bedtools and it worked just fine. I agree with you that it is nice to learn new ways of doing something and definitely writing your own scripts for a job is good practice for much needed skills. I will give you more direct feedback a little later about how well the script wo ...
written 9 days ago by paulotyama0
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Which SNPs fall within genes and what's their description?
... I have a bed file with 13k snps and want to intersect this with a gff file with all the genes annotated for this species. My aim is to find which of my snps fall within genes or other annotated features. Does any one have any suggestions on how to go about this? I'd really appreciate some suggestion ...
gene snp bed file gff file written 10 days ago by paulotyama0 • updated 10 days ago by Petr Ponomarenko730
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Comment: C: Extracting 200bp flanking sequence around a snp using Bedtools
... Nope, it works perfectly! I just had to format my genome file with a tab delimiter. ...
written 23 days ago by paulotyama0
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Comment: C: Extracting 200bp flanking sequence around a snp using Bedtools
... Thanks Goutham, I still get the same complaint even after I reformat both files as you suggested. Any more ideas? Thanks again, Paul ...
written 23 days ago by paulotyama0
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Comment: C: Extracting 200bp flanking sequence around a snp using Bedtools
... Thanks Igor. I reformatted the snp file as BED like you suggested and removed headers from the genome file but I still get the same complaint. Paul ...
written 23 days ago by paulotyama0
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Extracting 200bp flanking sequence around a snp using Bedtools
... Hi, I have been trying to use bedtools to extract 200bp flanking sequence around my snps bedtools slop -i snps.v03.bed -g Aradu.len.v02 -b 200 I get this error return instead Less than the req'd two fields were encountered in the genome file (Aradu.len.v02) at line 2. Exiting. What ...
bedtools extract snp flanking sequences written 24 days ago by paulotyama0 • updated 24 days ago by Goutham Atla6.9k

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