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532 results • Page
1 of 11
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DEGseq for multiple samples
DEGexp
DEGseq
just now by
ALOUSH ALI
• 0
0
votes
2
replies
17
views
BioInformatics, Software
BioInformatics
Learning
Softwares
updated 11 minutes ago by
barslmn
★ 1.5k • written 20 minutes ago by
hashim.rana11
• 0
0
votes
0
replies
8
views
Understanding Used Assembly: Why aren't authors specific about patch version?
GRCh38
gnomad
1000
assembly
genome
22 minutes ago by
JourneyToAbyss
▴ 200
0
votes
0
replies
11
views
METABOLOMICS DATA ANNOTATION
COMPOUND
METABOLOMICS
ANNOTATION
49 minutes ago by
Rishabh Jha
• 0
0
votes
0
replies
27
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
3 hours ago by
NikhilP
▴ 20
0
votes
1
reply
40
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 40 minutes ago by
barslmn
★ 1.5k • written 4 hours ago by
linnet.roque6
▴ 10
0
votes
0
replies
47
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
6 hours ago by
mbk0asis
▴ 660
0
votes
0
replies
43
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
7 hours ago by
Apprentice
▴ 140
0
votes
0
replies
111
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
4 hours ago by
Vincent Laufer
★ 2.8k
0
votes
0
replies
66
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
11 hours ago by
Chris
▴ 100
0
votes
0
replies
56
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 11 hours ago by
Ram
39k • written 11 hours ago by
Mah
• 0
1
vote
3
replies
146
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 11 hours ago by
GenoMax
129k • written 12 hours ago by
mls
• 0
0
votes
0
replies
65
views
snpEff error. No CDS checked
snpEff
gtf
WES
13 hours ago by
fifty_fifty
▴ 40
0
votes
0
replies
62
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
13 hours ago by
Maddie
• 0
0
votes
0
replies
62
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
13 hours ago by
rheab1230
▴ 140
1
vote
4
replies
157
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 11 hours ago by
Ram
39k • written 13 hours ago by
miguellarrazlopezdenovales
• 0
0
votes
0
replies
51
views
Pore-C-Snakemake output files
contacts
14 hours ago by
oksana03fel
• 0
1
vote
0
replies
69
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
13 hours ago by
fr
▴ 200
0
votes
2
replies
127
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 14 hours ago by
rpolicastro
12k • written 16 hours ago by
Pac314
▴ 10
0
votes
2
replies
106
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 hours ago by
survive
• 0
1
vote
1
reply
91
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 17 hours ago by
GenoMax
129k • written 18 hours ago by
hashim.rana11
• 0
1
vote
1
reply
105
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 4 hours ago by
Vincent Laufer
★ 2.8k • written 19 hours ago by
pilargmarch
▴ 80
0
votes
1
reply
88
views
Create customized gene annotation file
reference-genome
cellranger
updated 16 hours ago by
Ram
39k • written 23 hours ago by
rhonddaskl
• 0
0
votes
0
replies
68
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
23 hours ago by
aziznasr1920
• 0
1
vote
3
replies
113
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 40 minutes ago by
Pierre Lindenbaum
154k • written 23 hours ago by
herh
• 0
0
votes
0
replies
60
views
1000G reference panel for LD clumping
LD
1 day ago by
en_keser
• 0
0
votes
0
replies
77
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
1 day ago by
saladi
▴ 30
0
votes
2
replies
593
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 1 day ago by
Ram
39k • written 12 months ago by
Meeran
• 0
0
votes
7
replies
528
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 1 day ago by
Vincent Laufer
★ 2.8k • written 5 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
170
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 16 hours ago by
andres.firrincieli
3.3k • written 1 day ago by
kamanovae
▴ 80
0
votes
1
reply
138
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 1 day ago by
GenoMax
129k • written 1 day ago by
fafad046
• 0
0
votes
2
replies
138
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 1 day ago by
WouterDeCoster
47k • written 1 day ago by
Mohd
• 0
0
votes
2
replies
139
views
sorting BAM file
BAM
updated 22 hours ago by
ATpoint
72k • written 1 day ago by
Mohammad Amin
• 0
1
vote
0
replies
85
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 1 day ago by
Ram
39k • written 1 day ago by
bioinfo223
▴ 10
0
votes
0
replies
73
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 1 day ago by
zx8754
11k • written 1 day ago by
sidrah.maryam
▴ 50
0
votes
1
reply
136
views
Seurat: How to get all genes name of a cell ?
seurat
updated 1 day ago by
jv
★ 1.2k • written 1 day ago by
Picasa
▴ 640
1
vote
0
replies
215
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 1 day ago by
Ram
39k • written 1 day ago by
Supernova
• 0
0
votes
0
replies
96
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 1 day ago by
Ram
39k • written 1 day ago by
Fred
• 0
0
votes
1
reply
135
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 1 day ago by
Ram
39k • written 2 days ago by
chengc2016zzu
• 0
0
votes
0
replies
78
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
2 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
181
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
21 hours ago by
Pegasus
▴ 90
0
votes
0
replies
110
views
Merging multiple PLINK files
plink
merging
2 days ago by
Nejla
• 0
0
votes
0
replies
111
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 2 days ago by
GenoMax
129k • written 2 days ago by
keiko.asakura
• 0
0
votes
2
replies
210
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
1 day ago by
J.F.Jiang
▴ 900
0
votes
2
replies
186
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 2 days ago by
Ram
39k • written 2 days ago by
Joel Wallenius
▴ 120
1
vote
3
replies
693
views
Regular Expression for conversion
Linux
grep
updated 1 day ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
155
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 1 day ago by
Ram
39k • written 2 days ago by
barrypraveen
▴ 110
0
votes
2
replies
160
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
2 days ago by
pg45863
• 0
0
votes
1
reply
133
views
ABySS Process Killed
ABySS
genome
assembly
updated 2 days ago by
GenoMax
129k • written 2 days ago by
asarcillo
• 0
0
votes
0
replies
93
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
2 days ago by
narges.bioinf
• 0
532 results • Page
1 of 11
Recent Votes
A: GISTIC 2.0 Segment CN
A: GISTIC 2.0 Segment CN
GISTIC 2.0 Segment CN
GISTIC 2.0 Segment CN
A: WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs
WGCNA: Relating Eigenmodules to Clinical Traits Returns Matrix of NAs
Comment: including samples for which group is unknown to help adjust for another variable
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Recent Awards •
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Popular Question
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JourneyToAbyss
▴ 200
Popular Question
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Rishabh Jha
• 0
Teacher
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ATpoint
72k
Great Question
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linnet.roque6
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mbk0asis
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Recent Replies
Answer: BioInformatics, Software
by
barslmn
★ 1.5k
https://bio.tools/ is a great website indexing software used in bioinformatics.
Comment: BioInformatics, Software
by
Pierre Lindenbaum
154k
This is just too broad. what did you find so far ?
Answer: How to calculate kinship matrix table from vcf file
by
barslmn
★ 1.5k
You can use the vcftools relatedness2 module. Which implements the method describes in the paper: https://academic.oup.com/bioinformatics/a…
Answer: How to convert bed file to vcf?
by
Pierre Lindenbaum
154k
use AWK, change the header, body according to your needs... awk 'BEGIN {printf("##fileformat=VCFv4.2\n##INFO=<ID=END,Number=1,Type=I…
Comment: Doubt - installing LncTar software
by
Jeremiah
• 0
It is the full result, there is only one lncRNA and one mRNA in Examp1, and the output file is just like web version reult
Comment: How to get a comperative result of 2 bed files?
by
Pierre Lindenbaum
154k
convert the bed to vcf and use truvari.
Comment: bioinformatic analysis protocol performed by CD Genomics
by
barslmn
★ 1.5k
Mail their representative you talked with before or their support and ask them. There may not be a citable source. However, you can write t…
Comment: How to get a comperative result of 2 bed files?
by
herh
• 0
Actually, I am asked to use [truvari tool][1] but it works with vcf datasets. So, indeed I need a benchmarking measurement. One bed file is…
Comment: Building Dict File for GATK
by
dare_devil
★ 3.1k
Make sure that you have installed GATK in your system. Then follow the commands: For example, to generate `.dict` for `Homo_sapiens_assemb…
Comment: Precision-recall curve to compare metagenome classifiers to a gold standard - Is
by
sneha.d
• 0
Hi, I'm trying to construct a similar curve using Kraken2 and Bracken report files. I'm trying to use the sklearn.metrics.precision_recall_…
Comment: How to convert *.hic file to *.mcool file?
by
NikhilP
▴ 20
Thanks I'll check that too. Actually I found a way to add weight column in the converted mcool file by using cooler package.
Answer: What is NCBI Gene ID, where to find it and how to convert to entrez ID?
by
Pegasus
▴ 90
Hi, I am facing the exact issue, have u had luck to solve it ? If yes, please share here. Thanks
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★ 2.8k
whether or not you should conduct a pooled analysis or a stratified analysis depends upon the ratio of between-group variance to within-gro…
Answer: BAM creation - vg surject vs vg mpmap output
by
Rachel
• 0
From what I understand, there is indeed a difference. vg surject recomputes the alignment produced with the reference used to build the gra…
Comment: how to run FacetsSuite wrapper scripts on command line
by
GenoMax
129k
You need to replace `-foo --bar` with real options for the script. Those dummy names were just a demonstration of how you will provide thos…
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