User: FL512

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FL5120
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Posts by FL512

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Proper script to automate WGS analysis, typically bcftools
... Thank you very much! I do google it right away and sorry for the naive question. ...
written 15 days ago by FL5120
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Proper script to automate WGS analysis, typically bcftools
... Dear everyone, I have successfully extracted the necessary information by using below script; bcftools query -f '%CHROM \t%POS\n' sample1.vcf.gz > sample1.txt However, I have more than 100 samples in my hand, therefore, I wanted to automate this process with the below script; bcftools query -f ...
wgs automation bcftools linux written 16 days ago by FL5120
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Comment: C: Extract below 100% overlapping intervals among samples from WGS data
... Dear Pierre, Thank you very much for your quick & kind response. I appreciate it. I will give it a try tonight and let you know the results. ...
written 17 days ago by FL5120
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Extract below 100% overlapping intervals among samples from WGS data
... I am thinking about how I can extract shared overlap interval from WGS data with arbitrary percentage. According to the bedtools document, overlapping intervals can be extracted. https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html This is very useful and working well for me if I ...
bedtools wgs gatk written 17 days ago by FL5120 • updated 17 days ago by Pierre Lindenbaum134k
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Comment: C: Non-coding region of WGS
... Thank you for your help! ...
written 20 days ago by FL5120
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Comment: C: Non-coding region of WGS
... UPDATE: for someone like me, this is how I downloaded the region of interests. https://www.biostars.org/p/13290/ ...
written 4 weeks ago by FL5120
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Comment: C: Non-coding region of WGS
... Thank you for letting me know. By the way, how am I able to extract non-coding regions from my reference file, which I was struggling for a couple of days. I thought I had to download the non-UTR exons from UCSC genome browser. Anyway, thank you for your help! ...
written 5 weeks ago by FL5120
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Comment: C: Non-coding region of WGS
... Thank you very much. That was also I was thinking of but I did not know how to do it because of the lacking of knowledge and experience. I will keep you updated. Thank you again. ...
written 5 weeks ago by FL5120
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Non-coding region of WGS
... Dear all, I am new to work on WGS/WES analysis. I have VCF files obtained from WGS already and I would like to focus on SNPs located on non-coding regions such as promoter, enhancer, and 5'/3'-UTRs, or if possible, all non-coding regions I would like to analyze. 1. Is there any database, reference ...
non-coding region snp wgs written 5 weeks ago by FL5120

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