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questions
1
vote
1
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366
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
4 weeks ago by
Pierre Lindenbaum
161k
2
votes
8
replies
911
views
nfcore/fetchngs : Error: fasterq-dump cannot create this file
fasterq-dump
sra
sratools
fetchngs
updated 3 months ago by
pbioinf
▴ 70 • written 3 months ago by
Pierre Lindenbaum
161k
1
vote
2
replies
732
views
CDS phase 0,1,2 in GFF format
gff3
gff
cds
phasing
phase
8 months ago by
Pierre Lindenbaum
161k
25
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed
exome
agilent
next-gen
written 11.4 years ago by
Pierre Lindenbaum
161k
5
votes
5
replies
1.2k
views
multiqc: group samples by population + boxplot ?
multiqc
updated 9 weeks ago by
Phil Ewels
★ 1.4k • written 10 months ago by
Pierre Lindenbaum
161k
3
votes
1
reply
695
views
How do I use the new human pangenome reference to discover SNV and SV.
pangenome
reference
graph
vg
11 months ago by
Pierre Lindenbaum
161k
0
votes
1
reply
665
views
UKBiobank / DNANexus. Working with WDL and directories.
wdl
workflow
dnanexus
ukbiobank
14 months ago by
Pierre Lindenbaum
161k
3
votes
1
reply
649
views
htslib/c what is the correct way to use bgzf_thread_pool ?
fastq
multithread
htslib
C
15 months ago by
Pierre Lindenbaum
161k
3
votes
5
replies
1.4k
views
Implementing a custom java class in nextflow files.
groovy
nf
java
nextflow
16 months ago by
Pierre Lindenbaum
161k
10
votes
9
replies
3.4k
views
6 follow
Why piping a conda command into bash doesn't work ?
makefile
bash
conda
updated 2.1 years ago by
Istvan Albert
100k • written 2.1 years ago by
Pierre Lindenbaum
161k
1
vote
1
reply
1.1k
views
rvtests : all genes are "Gene xxx has 0 variants, skipping"
rvtests
gene
vcf
2.3 years ago by
Pierre Lindenbaum
161k
9
votes
3
replies
3.6k
views
nextflow DSL2: best practice to design and reuse a process/worfklow
dsl2
nextflow
workflow
updated 2.4 years ago by
ATpoint
82k • written 2.4 years ago by
Pierre Lindenbaum
161k
11
votes
10
replies
2.1k
views
Searching for mRNA ending with a specific 3' pattern in NON-poly-A RNASeq data.
rnaseq
poly-a
2.6 years ago by
Pierre Lindenbaum
161k
3
votes
5
replies
2.5k
views
Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome"
Hi-C
intervals
chromosome
interaction
tad
updated 5.3 years ago by
Devon Ryan
104k • written 5.3 years ago by
Pierre Lindenbaum
161k
3
votes
3
replies
4.1k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl
mysql
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
1
vote
2
replies
1.1k
views
"GSAT_MM" repeats in mm10
repeat
microsattelite
mouse
musmusculus
3.5 years ago by
Pierre Lindenbaum
161k
3
votes
5
replies
1.3k
views
Finding structural variants after Spades
spades
vg
sv
updated 3.6 years ago by
samuel.a.odonnell
▴ 520 • written 3.7 years ago by
Pierre Lindenbaum
161k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
13
votes
3
replies
8.4k
views
Naming Chromosomes: From Ncbi Nc_0000Abc To Ucsc Chrabc
chromosome
ncbi
updated 4.2 years ago by
vkkodali_ncbi
★ 3.7k • written 11.7 years ago by
Pierre Lindenbaum
161k
13
votes
4
replies
8.5k
views
Adding An Extra Column To A Vcf File.
vcf
format
next-gen
sequencing
updated 4.2 years ago by
Biostar
20 • written 14.0 years ago by
Pierre Lindenbaum
161k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
10
votes
5
replies
2.5k
views
structural variants in gnomad and the VCF spec. Why is tabix/bcftools failing ?
vcf
specification
gnomad
sv
structural variant
updated 4.9 years ago by
John Marshall
3.0k • written 4.9 years ago by
Pierre Lindenbaum
161k
6
votes
20
replies
2.4k
views
longranger mkfastq : "unrecognised option '--qc' "
longranger
mkfastq
updated 4.9 years ago by
GenoMax
141k • written 4.9 years ago by
Pierre Lindenbaum
161k
41
votes
13
replies
12k
views
9 follow
The Longest Chromosome > Sizeof(Int32)
chromosome
database
length
updated 5.3 years ago by
michael.ante
★ 3.8k • written 12.6 years ago by
Pierre Lindenbaum
161k
2
votes
4
replies
2.7k
views
getting the HOM_REF genotypes using bcftools mpileup+call ?
bcftools
call
mpileup
variant
genotype
updated 5.3 years ago by
Ram
43k • written 5.3 years ago by
Pierre Lindenbaum
161k
3
votes
1
reply
1.4k
views
GNU autotools and samtools/htslib
autotools
configure
samtools
htslib
c
updated 5.6 years ago by
John Marshall
3.0k • written 5.6 years ago by
Pierre Lindenbaum
161k
8
votes
2
replies
4.6k
views
Impute: File Formats ?
haplotype
ped
linkage
updated 5.6 years ago by
Ram
43k • written 13.8 years ago by
Pierre Lindenbaum
161k
2
votes
5
replies
3.1k
views
Can You Improve This Erlang Code ? (Was "Average Length Of The Sequences In A Fasta File")
code
fasta
sequence
functional
updated 5.6 years ago by
Ram
43k • written 13.8 years ago by
Pierre Lindenbaum
161k
3
votes
3
replies
2.4k
views
Anyone Using Jboss Drools ?
workflow
updated 5.6 years ago by
Ram
43k • written 13.8 years ago by
Pierre Lindenbaum
161k
10
votes
6
replies
2.7k
views
What Is The Index Of The First Base In Pph2 ? 0 Or 1 ?
mutation
prediction
index
updated 5.6 years ago by
Ram
43k • written 13.9 years ago by
Pierre Lindenbaum
161k
10
votes
2
replies
5.5k
views
Bwa: Number Of Threads
bwa
next-gen
sequencing
parallel
hardware
updated 5.6 years ago by
Ram
43k • written 13.9 years ago by
Pierre Lindenbaum
161k
11
votes
6
replies
5.1k
views
Ncbi Esearch :Searching For Snp/Genes/... At In A Given Segment Chr:Start-End ?
search
ncbi
eutils
updated 5.6 years ago by
Ram
43k • written 13.9 years ago by
Pierre Lindenbaum
161k
5
votes
7
replies
2.5k
views
Length(Ucsc/Ensgene) % 3 != 0
protein
ucsc
cdna
translation
sequence
updated 2.6 years ago by
Ram
43k • written 13.9 years ago by
Pierre Lindenbaum
161k
16
votes
6
replies
5.2k
views
The 'Bin' Column Used By Sam, Ucsc...
database
index
updated 5.7 years ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
161k
16
votes
3
replies
4.4k
views
A Grep For Gene Ontology ?
gene
GO
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
5
votes
5
replies
4.5k
views
Mapping One Repeat (37Pb) With Bwa/Maq
bwa
next-gen
sequencing
mapping
updated 5.7 years ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
18
votes
21
replies
6.8k
views
Anyone Using "Biomart + Java Web Services" ?
biomart
java
webservice
updated 5.7 years ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
10
votes
9
replies
4.3k
views
8 follow
Estimating cross contamination in a set of BAMS
contamination
bam
updated 5.9 years ago by
igor
13k • written 5.9 years ago by
Pierre Lindenbaum
161k
3
votes
5
replies
1.7k
views
extract_sv_reads/samblaster: explain this code please.
samblaster
c
cpp
spliced-read
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Pierre Lindenbaum
161k
13
votes
6
replies
5.8k
views
Geo Profiles: Downloading Profile Data.
geo
ncbi
api
updated 6.4 years ago by
Biostar
20 • written 13.2 years ago by
Pierre Lindenbaum
161k
4
votes
4
replies
5.0k
views
Gatk Pipeline: Markduplicates At The End ?
gatk
next-gen
bam
markduplicates
pipeline
workflow
duplicates
updated 6.5 years ago by
Biostar
20 • written 11.5 years ago by
Pierre Lindenbaum
161k
4
votes
5
replies
2.0k
views
Explain fig. 5 c of "The impact of rare variation on gene expression across tissues" doi:10.1038/nature24267
rare
variant
article
paper
expression
updated 6.5 years ago by
aditi.qamra
▴ 270 • written 6.5 years ago by
Pierre Lindenbaum
161k
17
votes
5
replies
4.4k
views
Describe Your Architecture: Uniprot
uniprot
java
database
updated 6.6 years ago by
navela78
▴ 70 • written 11.2 years ago by
Pierre Lindenbaum
161k
41
votes
15
replies
13k
views
9 follow
Should I Remove The Unmapped Reads From My Bam ?
samtools
next-gen
sequencing
bam
short
updated 6.6 years ago by
Karma
▴ 310 • written 12.2 years ago by
Pierre Lindenbaum
161k
0
votes
5
replies
2.6k
views
URL for NCBI Efetch + XML with full annotation table
xml
ncbi
efetch
annotation
eutils
updated 6.9 years ago by
GenoMax
141k • written 6.9 years ago by
Pierre Lindenbaum
161k
105
votes
21
replies
21k
views
19 follow
Why Should I Use Galaxy ?
galaxy
workflow
7.0 years ago by
Pierre Lindenbaum
161k
116
votes
25
replies
70k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 14 months ago by
Miguel
▴ 20 • written 13.3 years ago by
Pierre Lindenbaum
161k
21
votes
4
replies
8.8k
views
What'S The Difference Between Two Versions Of The Same Assembly ?
genome
sequence
ncbi
updated 7.5 years ago by
Biostar
20 • written 13.4 years ago by
Pierre Lindenbaum
161k
0
votes
2
replies
2.5k
views
Cleaning FASTQ files containing a contamination sequence.
fastq
updated 7.6 years ago by
lexnederbragt
★ 1.3k • written 7.6 years ago by
Pierre Lindenbaum
161k
8
votes
4
replies
2.3k
views
Implementing a naive javascript-based de Bruijn graph
debruijn
graph
javascript
algorithm
7.9 years ago by
Pierre Lindenbaum
161k
141 results • Page
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