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31 results • Page
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4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 1 hour ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
7
replies
521
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 19 hours ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
Camilo Andres
▴ 30
1
vote
4
replies
104
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 2 hours ago by
Ram
39k • written 4 hours ago by
miguellarrazlopezdenovales
• 0
0
votes
3
replies
64
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 2 hours ago by
GenoMax
129k • written 2 hours ago by
mls
• 0
0
votes
3
replies
165
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 7 hours ago by
andres.firrincieli
3.3k • written 1 day ago by
kamanovae
▴ 80
0
votes
3
replies
717
views
How can I use KING on windows ?
plink
king
updated 7 hours ago by
Ram
39k • written 4.0 years ago by
gwas_maniac
▴ 20
0
votes
2
replies
96
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 5 hours ago by
rpolicastro
12k • written 7 hours ago by
Pac314
▴ 10
0
votes
2
replies
518
views
1-way-2-fold cross family analysis
cross-family-analysis
updated 5 hours ago by
Ram
39k • written 3.8 years ago by
sinha.shriprakash
▴ 20
0
votes
2
replies
136
views
sorting BAM file
BAM
updated 13 hours ago by
ATpoint
72k • written 1 day ago by
Mohammad Amin
• 0
1
vote
2
replies
177
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
12 hours ago by
Pegasus
▴ 90
0
votes
2
replies
135
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 15 hours ago by
WouterDeCoster
47k • written 1 day ago by
Mohd
• 0
0
votes
2
replies
203
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
20 hours ago by
J.F.Jiang
▴ 900
0
votes
1
reply
67
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 8 hours ago by
GenoMax
129k • written 9 hours ago by
hashim.rana11
• 0
0
votes
1
reply
61
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
updated 7 hours ago by
Raony Guimarães
★ 1.2k • written 8 hours ago by
survive
• 0
0
votes
1
reply
78
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 12 hours ago by
Pierre Lindenbaum
154k • written 14 hours ago by
herh
• 0
0
votes
1
reply
1.2k
views
Best tool for bacterial genomic island prediction?
genome
genomic-island
updated 5 hours ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
1
reply
71
views
Create customized gene annotation file
reference-genome
cellranger
updated 7 hours ago by
Ram
39k • written 13 hours ago by
rhonddaskl
• 0
1
vote
1
reply
3.0k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 1 hour ago by
sackettl
▴ 20 • written 6.9 years ago by
maria.segovia.ramirez
▴ 10
0
votes
0
replies
862
views
Error processing Hi-data using HiCUP
NGS
HiCUP
Hi-C
updated 6 hours ago by
Ram
39k • written 4.0 years ago by
srhic
▴ 40
0
votes
0
replies
72
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
22 hours ago by
saladi
▴ 30
0
votes
0
replies
49
views
1000G reference panel for LD clumping
LD
14 hours ago by
en_keser
• 0
0
votes
0
replies
51
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
13 hours ago by
aziznasr1920
• 0
0
votes
0
replies
163
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
23 hours ago by
Vincent Laufer
★ 2.8k
0
votes
0
replies
31
views
Pore-C-Snakemake output files
contacts
5 hours ago by
oksana03fel
• 0
0
votes
0
replies
32
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
4 hours ago by
rheab1230
▴ 140
0
votes
0
replies
35
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
4 hours ago by
Maddie
• 0
0
votes
0
replies
38
views
snpEff error. No CDS checked
snpEff
gtf
WES
4 hours ago by
fifty_fifty
▴ 40
1
vote
0
replies
52
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
3 hours ago by
fr
▴ 200
0
votes
0
replies
21
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
2 hours ago by
Chris
▴ 100
0
votes
0
replies
23
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 2 hours ago by
Ram
39k • written 2 hours ago by
Mah
• 0
0
votes
0
replies
62
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
1 hour ago by
pilargmarch
▴ 80
31 results • Page
1 of 1
Recent Votes
Problem with PGDSpider v 2.1.0.2
Comment: Filter VCF file for variant alleles
Help making ADMIXTURE output digestible
Answer: Graphing Average Expression of Group of Genes
Linear models with limma: coefficients not estimatable, are the others OK?
Answer: How to find gene annotation given a position in a bacterial genome
Comment: INSTALLING DEseq2 via conda
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Answer: Manhattan Plot with independent significant hits
by
Vincent Laufer
★ 2.8k
Consider using [locuszoom][1] for genomic regions small enough to warrant special clarification that the two associations are independent. …
Comment: Problem with PGDSpider v 2.1.0.2
by
sackettl
▴ 20
I have this same problem with version 2.1.1.5. Did you ever find a solution?
Comment: Filter VCF file for variant alleles
by
Ram
39k
> can't find anything to do this It's in there. If you had looked a little deeper, you would have found - on your own - exactly what Pierr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
GenoMax
129k
Then create an alternate Reference with data for the sample: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateR…
Comment: Help making ADMIXTURE output digestible
by
Aaron
▴ 10
You can also check out [pong][1] (README [here][2]), which creates interactive plots with the clusters and colors automatically aligned acr…
Comment: To call variants can I use my aligned WGS data as a reference genome
by
mls
• 0
Yes they are but I wanna compare one of my samples with others , rather S288C.
Comment: To call variants can I use my aligned WGS data as a reference genome
by
Pierre Lindenbaum
154k
the bam are mapped on S288C fasta isn't it ? why would you need another reference ?
Comment: Filter VCF file for variant alleles
by
Pierre Lindenbaum
154k
use a filtering expression https://samtools.github.io/bcftools/bcftools.html#expressions , something like; bcftools view -i 'COUNT(GT=…
Comment: Filter VCF file for variant alleles
by
miguellarrazlopezdenovales
• 0
I've tried bcftools, which seems to be the closest I've got, but I can't find anything to do this. I have also found vcftools --max-non-ref…
Comment: Filter VCF file for variant alleles
by
Ram
39k
What have you tried? You've mentioned bcftools as a tag, have you read the manual?
Comment: How to concatenate multiple fasta file
by
doggie
• 0
@shenwei356 Thank you so much! Your prompt reply helped me a lot!
Answer: PacBio Pipeline and Tools for Variant Call
by
William Rowell
▴ 250
> What are Quality parameters that should be taken care ( Adapter trim, Reads filter, Min Data size, ) How to trim adapter, What tools to u…
Comment: Ambient RNA expression correction
by
rpolicastro
12k
Ambient RNA would have the same cell barcode as a valid cell-containing droplet since the RNA gets partitioned into the droplet with the ce…
Comment: Can any one suggest tools that generate "mind-maps" on concepts in biology/biote
by
Vincent Laufer
★ 2.8k
sorry to be blunt but this question is so broad i worry it may not evoke a cogent answer. you might start by finding a review on the use …
Answer: Can any one suggest tools that generate "mind-maps" on concepts in biology/biote
by
Jesse
▴ 550
Haven't used it, but I've heard good things about [Obsidian](https://obsidian.md/) as a note-taking tool, and it has [graphing features](ht…
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