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questions
0
votes
0
replies
335
views
Get SNPs with MAF 0.05 for all genes - attempt with BiomaRt
BiomaRt
SNPs
MAF
genes
17 months ago by
camerond
▴ 190
2
votes
2
replies
3.1k
views
Seurat - label cells in cluster plot by transcripts per cell
Seurat
RNA-Seq
single-cell
cluster labelling
updated 3.5 years ago by
rpolicastro
13k • written 3.5 years ago by
camerond
▴ 190
5
votes
10
replies
4.0k
views
Snakemake - moving, re-naming, unzipping and merging files for downstream analysis
snakemake
merging
fastq
python
3.8 years ago by
camerond
▴ 190
2
votes
4
replies
3.7k
views
Using bedtools intersect on multiple bed files to retain peaks in 2 out of 3 files
bed
bedtools
updated 13 months ago by
Ram
43k • written 4.5 years ago by
camerond
▴ 190
6
votes
8
replies
1.6k
views
Extracting high quality reads from partially failed 10X single cell RNA-, ATAC-seq sequencing run
single cell RNA-seq
10X
sequencing
4.2 years ago by
camerond
▴ 190
4
votes
2
replies
4.1k
views
Snakemake: Force execution of rules in a specific order - ignoring wildcards
snakemake
python
rule execution
updated 4.2 years ago by
Eric Lim
★ 2.1k • written 4.2 years ago by
camerond
▴ 190
0
votes
0
replies
1.2k
views
One tool for get genome co-ordinates from rsIDs GWAS sumstats files, then liftOver from hg18 to hg19?
liftover
GWAS sumstats
linux
SNP
4.8 years ago by
camerond
▴ 190
2
votes
3
replies
2.2k
views
Appropriate use of wildcards for single instances in Snakemake
Snakemake
wildcards
Garfield
updated 4.9 years ago by
Jeremy Leipzig
22k • written 4.9 years ago by
camerond
▴ 190
6
votes
3
replies
956
views
Extract and retain only chromosome info in GWAS sumstats file
bash
GWAS sumstats
awk
sed
munging
updated 5.0 years ago by
shawn.w.foley
★ 1.3k • written 5.0 years ago by
camerond
▴ 190
4
votes
2
replies
2.8k
views
Snakemake logging error
snakemake
log
5.0 years ago by
camerond
▴ 190
5
votes
5
replies
2.0k
views
Issue running deeptools on cluster via snakemake
Deeptools
Snakemake
updated 5.0 years ago by
russhh
5.7k • written 5.0 years ago by
camerond
▴ 190
1
vote
2
replies
4.3k
views
Problems when exporting GRanges file as bigwig after hg38 to hg19 lift over using rtracklayer and annotation hub
R
lift over
rtracklayer
GRanges
bigwig
updated 5.1 years ago by
benformatics
3.9k • written 5.1 years ago by
camerond
▴ 190
21
votes
15
replies
9.0k
views
8 follow
Obtaining rsIDs using BiomaRt or linux
R
Biomart
rsID
SNPs
bed
updated 2.2 years ago by
Nance
• 0 • written 5.9 years ago by
camerond
▴ 190
12
votes
22
replies
9.0k
views
Get rsID for a list of SNPs in an entire GWAS sumstats file
next-gen
sequencing
GWAS
sumstats
updated 2.7 years ago by
AVA
▴ 40 • written 6.1 years ago by
camerond
▴ 190
15
votes
6
replies
24k
views
Extract ONLY chromosomes 1-22 from bam file - removing extraneous chr annotations
genome
next-gen
sequencing
bam file filtering
updated 6.2 years ago by
Pierre Lindenbaum
161k • written 6.2 years ago by
camerond
▴ 190
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