User: rodd

gravatar for rodd
rodd40
Reputation:
40
Status:
New User
Location:
London, United Kingdom
Last seen:
3 hours ago
Joined:
4 years, 3 months ago
Email:
r***************@gmail.com

Posts by rodd

<prev • 25 results • page 1 of 3 • next >
0
votes
0
answers
9.6k
views
0
answers
Comment: C: Converting SNP from chr:pos to rs number using PLINK?
... I think it's end, but double check it on UCSC browser by viewing your SNP of interest. ...
written 4 hours ago by rodd40
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Generating heatmaps of pre-selected candidate genes after deseq2
... How do you "slice the matrix of normalized counts to contain only interesting genes", considering a list/data frame named "GENES_TO_LABEL" (containing the names of the genes you wish to label) which you've imported from a txt file? ...
written 10 days ago by rodd40
2
votes
3
answers
9.0k
views
3
answers
Answer: A: How To Separate Snp Variants From Indel Variants In The Same Vcf File
... You can separate single nucleotide variants from indels using [vcftools][1] and the flags `--keep-only-indels` or `--remove-indels` vcftools --vcf input_file_containing_all_variants.vcf --remove-indels --recode --recode-INFO-all --out output_file_with_indels_removed.vcf [1]: https://vcftoo ...
written 27 days ago by rodd40
0
votes
1
answer
107
views
1
answer
Is there a FASTA file containing 1000 Genomes variant information to check reference alleles in VCF files?
... Hi folks! I've imputed genotype data using the Michigan Imputation Server (MIS), using the 1000 Genomes Phase 1 panel (not many errors were found, according to MIS). After (and before) imputation, I wanted to perform a sanity check by running checkVCF.py [https://github.com/zhanxw/checkVCF], to mak ...
1000 genomes reference allele checkvcf written 4 weeks ago by rodd40 • updated 13 days ago by chrchang5235.3k
0
votes
5
answers
5.7k
views
5
answers
Comment: C: Filtering Imputation output: how to filter on a VCF INFO field
... Thanks for this comment @Sunshine n Rain, it's nice and easy to filter out SNPs from vcf files according to MAF and R2 values using this command!! ...
written 4 weeks ago by rodd40
0
votes
0
answers
9.6k
views
0
answers
Comment: C: Converting SNP from chr:pos to rs number using PLINK?
... Hi all! I don't know if this is a more recent thing, but I was not able to download the file using the method described here, because the download times out as the file is too big for the table browser. I found the file containing all SNPs in the UCSC directory ( http://hgdownload.cse.ucsc.edu/golde ...
written 4 weeks ago by rodd40
0
votes
2
answers
752
views
2
answers
Answer: A: how to unzip Michigan imputation server output compressed folder
... (Just expanding on Molly_K's answer) If extracting files in a cluster, install 7zip using conda conda install -c bioconda p7zip Then extract multiple files (individual chromosomes) using 7zip, and include password in the command for i in {1..22}; do 7z e chr_$i.zip -pPASSWORD; done . ...
written 4 weeks ago by rodd40
0
votes
1
answer
666
views
1
answers
Comment: C: how to check if SNP falls in the exon region
... I've been looking for this R code for such a long time!! Thanks @cpad0112!! ...
written 10 weeks ago by rodd40
0
votes
2
answers
3.3k
views
2
answers
Comment: C: deseq2 user defined size factors
... Ooops. I guess it's better I don't do that, actually. Looks like it's better to just use the whole dataset, and perform multiple testing correction on the list of genes I am interested, as it seems tricky to stipulate size factors from one dds object to another. Source: [https://support.bioconductor ...
written 10 weeks ago by rodd40
0
votes
2
answers
3.3k
views
2
answers
Comment: C: deseq2 user defined size factors
... How is this then passed onto another dds object? (I am trying to analyse only a subset of genes from all genes expressed in a dataset because I am focusing on genes which are modulated by eQTLs - but ideally I would like to normalise raw counts to the size factors calculated using the whole dataset ...
written 10 weeks ago by rodd40

Latest awards to rodd

Supporter 7 months ago, voted at least 25 times.
Epic Question 2.1 years ago, created a question with more than 10,000 views. For trimming fastq files with Trimmomatic
Great Question 2.3 years ago, created a question with more than 5,000 views. For trimming fastq files with Trimmomatic
Popular Question 3.8 years ago, created a question with more than 1,000 views. For trimming fastq files with Trimmomatic

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1518 users visited in the last hour