User: camerond

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camerond10
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Posts by camerond

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Comment: C: Obtaining rsIDs using BiomaRt or linux
... Hi @dan_adams Thanks for your response. This suggestion ran for a bit (it takes a while) but after 28 SNPs it threw the following error: Error in `[<-.data.frame`(`*tmp*`, , 5, value = 27L) : replacement has 1 row, data has 0 It's obviously choking as the SNP does not correspond to an ...
written 3 months ago by camerond10
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Obtaining rsIDs using BiomaRt or linux
... I have a list of 390 SNPs that I need to retrieve rsIDs for on the hg19 build. My SNP file is in the following bed format (chromosome start stop). chr1 207679307 207679307 chr1 207684192 207684192 chr1 207685786 207685786 chr1 207685965 207685965 chr1 207692049 207692049 ...
R biomart snps rsid bed written 3 months ago by camerond10 • updated 3 months ago by Pierre Lindenbaum112k
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi finswimmer, Finally got it working and accepted your answer. Thanks for your help. The final issue I was having was with the zipped dbSNP file. When trying to index with tabix it was throwing an error. Zipping had to be done with bgzip, I'd used something else to zip the file initially. The fin ...
written 5 months ago by camerond10
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi finswimmer, I have tried your suggestion (pre-update), Alex's and several other methods (including bcftools). The issue I was having with your suggestion is with java. I'd never used Java before, and had issues getting `snpSift` to work. Tbh I didn't give it a huge amount of time, as I was mor ...
written 5 months ago by camerond10
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi Alex, Thanks for the update. I still can't get this working unfortunately. I altered my sumstats file using both awk commands, as I'm unsure if the sumstats file is 0 or one based, and ran them separately. Full header of sumstats pre-awk: MarkerName Allele1 Allele2 Effect StdErr P.value ...
written 5 months ago by camerond10
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi Alex, Thanks for the response. Just getting round to this now as I was off for Easter. I had a couple of minor issues with the `sort-bed` command. Firstly it didn't like the header: Non-numeric start coordinate. See line 1 in answer.bed. (remember that chromosome names should not co ...
written 5 months ago by camerond10
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Comment: C: Get rsID for a list of SNPs in an entire GWAS sumstats file
... Hi Fin swimmer, Yes, Allele 1 is always the REF allele. There are also separate columns for each allele in the sumstats file. The Allele1 column refers to the reference allele and this corresponds the last allele quoted in the MarkerName column (col 1): MarkerName Allele1 Allele2 Effect StdEr ...
written 6 months ago by camerond10
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Get rsID for a list of SNPs in an entire GWAS sumstats file
... I have downloaded a GWAS sumstats file and have a list of SNP locations. The information for each SNP location is condensed in column 1 of the sumstats file in the following format: 1:100000012_G_T - 1 = Chromosome - 100000012 = SNP location - T = Allele 1 - G = Allele 2 I'm trying to r ...
sequencing gwas next-gen sumstats written 6 months ago by camerond10 • updated 6 months ago by cpad01129.0k
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Comment: C: Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotation
... Thanks for your responses. I implemented the second suggestion as it had fewer steps and worked fine, all reads were removed. I can use that one liner in my pipeline, thanks again. I'll have a go using the downstream package and see if it likes the header or not. ...
written 6 months ago by camerond10
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Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
... I've wrote this multi-facted question to solve a specific coding problem, but also to bring together information that is covered partially across multiple existing biostars posts that others may find useful. Part 1 - Edit the bam file ------ I have several bam files that have reads mapped to chro ...
genome sequencing next-gen bam file filtering written 6 months ago by camerond10 • updated 6 months ago by Pierre Lindenbaum112k

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