User: Huichen03

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Huichen0310
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12 months ago
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Posts by Huichen03

<prev • 10 results • page 1 of 1 • next >
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sort the homo sapiens genes by chromosome with Unix command lines
... Hi, I want to sort homo sapiens gene by chromosome. I tried with `sort -t _ -k 3 -g genes.txt > genes_by_chr.txt`, while the result is not what I want. In my genes.txt file, the chromosome column includes numbers like 1, 2, 3 ... and characters like CHR_HG1_PATCH, CHR_HG26_PATCH, and GL000009.2. ...
gene sort written 10 months ago by Huichen0310
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How to deal with rsIDs that not include in dbSNP
... Hi, I am trying to get annotations for all my rsIDs. After analysis by *BiomaRt*, I found that not all of my rsIDs were annotated. I understand that some of the rsIDs are not in the genes, and for those SNPs that do not in the genes, my result table showed the rsIDs and kept the gene column blank. ...
biomart snp written 10 months ago by Huichen0310 • updated 10 months ago by Emily_Ensembl18k
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Understand the chromosome name in homo sapiens gene database
... Hi, I am new to bioinformatics. I am trying to understand the meaning of chromosome column. Except for the common 22 pairs of chromosome and X, Y, some other chromosome names are strange to me like CHR_HSCHR17_2_CTG5, MT, CHR_HSCHR8_3_CTG1, CHR_HSCHR7_3_CTG4_4... Could you please advise some intro ...
gene chromosome written 10 months ago by Huichen0310 • updated 10 months ago by Bastien Hervé4.0k
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Comment: C: How to get million target snps info(ie. chromosome, location) in a easy way?
... Hi, Thank you for your advice. When searching on a file of IDs, should the command line be $ grep -f? If I use $ grep -fF, I will have the error that grep: F: No such file or directory. ...
written 11 months ago by Huichen0310
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How to get million target snps info(ie. chromosome, location) in a easy way?
... Hi all, I am trying to get SNP locations. What I have done is that downloaded the dbsnp database in the ensembl and used the command line `grep -f snps.txt homo_sapiens_snp.vcf > matches.vcf` to get my target SNP info. There are about two million SNPs in my snps.txt, and all snps info in dbsnp d ...
gene snp written 11 months ago by Huichen0310 • updated 11 months ago by finswimmer11k
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Where can I download a txt file including all human snps rsids, chromosome, and locations?
... I tried to download data from useast.ensemble.org, while the downloaded file only contains SNPs in chromosome 1. Is there a better way to do that? Thank you in advance! ...
gene R snp written 11 months ago by Huichen0310 • updated 11 months ago by genomax65k
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snp annotation using BiomaRt
... Hi, I want to get the gene names from 2400000 snps using BiomaRt in R. But since the snps size is huge, I could not get the result of these snps' annotation for one time. Do you guys have any other suggestions? Thank you in advance! ...
gene R biomart snp written 11 months ago by Huichen0310 • updated 11 months ago by Emily_Ensembl18k
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Comment: C: using biomaRt in R to annotate SNPs to Genes within 1000kb
... Got it. Thanks a lot! ...
written 12 months ago by Huichen0310
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Comment: C: using biomaRt in R to annotate SNPs to Genes within 1000kb
... Hi, I am working on this problem also. When I followed the step 4 using findOverlaps function in GenomicRanges, a mistake popped out. `> findOverlaps( snp.gr, annot.gr, maxgap = 1000) Hits object with 102300 hits and 0 metadata columns: queryHits subjectHits [1 ...
written 12 months ago by Huichen0310
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Where can I download homo sapiens gene locations file including ensembl gene id, chr, start and end?
... I am trying to use GRange for mapping snps to gene around 100kb. But I do not know how to download homo sapiens gene locations file including ensembl gene id, chr, start and end? Thank you in advance! ...
gene biomart snp written 12 months ago by Huichen0310 • updated 12 months ago by JJ430

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