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168 results • Page
1 of 4
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0
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0
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14
views
NCBI vs Ensembl - Ortholog genes Information
Genomics
Orthologs
NCBI
Ensembl
updated 32 minutes ago by
Pierre Lindenbaum
162k • written 33 minutes ago by
José
▴ 10
1
vote
1
reply
49
views
when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam
htslib
updated 52 minutes ago by
Pierre Lindenbaum
162k • written 2 hours ago by
Aaron
▴ 10
0
votes
0
replies
33
views
Why does WGCNA use weighted correlation instead of Pearson correlation?
wgcna
2 hours ago by
絶望燃やし
• 0
0
votes
5
replies
117
views
I cannot download VG in any way
vg
vgteam
updated 2 hours ago by
GenoMax
142k • written 4 hours ago by
gforg34
• 0
0
votes
0
replies
31
views
reference geome gaf file obsolent GO replacement
gaf
GO
4 hours ago by
Nicolas
• 0
0
votes
1
reply
69
views
Can I count UMI-barcode combination without mapping?
HyDrop
protein
UMI
UMI-Tools
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
104
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
5 hours ago by
Jack
• 0
0
votes
4
replies
689
views
Illumina EPIC v2 IlmnIDs and probe names
Illumina
EPIC
EPICv2
updated 6 hours ago by
Papyrus
★ 2.9k • written 6 months ago by
christine.a.pedersen
▴ 10
3
votes
5
replies
176
views
Best practices in Fungal Genome Assembly
illumina
assembly
nanopore
genome
updated 3 hours ago by
samuel.a.odonnell
▴ 540 • written 8 hours ago by
Umer
▴ 50
0
votes
1
reply
119
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
updated 7 hours ago by
GenoMax
142k • written 10 hours ago by
Ian
6.0k
2
votes
1
reply
124
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated 8 hours ago by
ATpoint
82k • written 10 hours ago by
ev97
▴ 20
1
vote
8
replies
326
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 5 hours ago by
SamGG
▴ 20 • written 21 hours ago by
vmpsb
• 0
0
votes
0
replies
57
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
11 hours ago by
Manko47
• 0
3
votes
7
replies
435
views
Z score
Z-score
updated 10 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
1
vote
2
replies
148
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
8 hours ago by
ashaneev07
▴ 20
2
votes
2
replies
336
views
Annotating single cell data automatically
single-cell
updated 13 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
0
votes
0
replies
57
views
EXOME DEPTH - CNV
CNV
13 hours ago by
Neha
• 0
0
votes
2
replies
107
views
coding and non-coding region of the viral genome
viral-genome
40 minutes ago by
Ghada
• 0
2
votes
2
replies
107
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 5 hours ago by
Ram
44k • written 14 hours ago by
Clark_BioMorgan
▴ 50
0
votes
2
replies
150
views
Salmon ~ Effective Length
Salmon
updated 8 hours ago by
GenoMax
142k • written 18 hours ago by
chrisk
• 0
2
votes
3
replies
226
views
Search within posts based on tags using the Biostars API
api
meta
updated 5 hours ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
0
votes
0
replies
64
views
Funcotator gnomAD incoherent number of output fields
gatk
gnomAD
Funcotator
updated 5 hours ago by
Ram
44k • written 18 hours ago by
jaime alvarez
▴ 30
0
votes
1
reply
127
views
Help with proteomics downstream analysis
mass-spectrometry
proteomics
updated 17 hours ago by
Ram
44k • written 1 day ago by
Álvaro
• 0
0
votes
2
replies
108
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
28 minutes ago by
Ngrin
• 0
0
votes
0
replies
65
views
Calculating F_IS, F_IT on ancient DNA
adna
21 hours ago by
devenvyas
▴ 740
0
votes
0
replies
65
views
The number of region with the motif sequence is different between HOMER outputs
findMotifsGenome
HOMER
annotatePeaks
22 hours ago by
Aki
▴ 20
3
votes
3
replies
855
views
Cut&Run and heatmap
MACS2
bowtie2
updated 5 hours ago by
Ram
44k • written 13 months ago by
qudrat.nii
▴ 10
3
votes
12
replies
5.3k
views
7 follow
txt file to bigwig
MEME
bigwig
updated 5 hours ago by
GenoMax
142k • written 8.6 years ago by
tanni93
▴ 50
2
votes
2
replies
204
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 11 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
2
replies
132
views
identify the coordinate for coding and non_coding region.
coding
non_coding
1 day ago by
Ghada
• 0
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 1 day ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
3
votes
2
replies
151
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 11 hours ago by
zx8754
11k • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
185
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
12 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
111
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
updated 2 hours ago by
Ram
44k • written 1 day ago by
Ghada
• 0
3
votes
7
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 2 hours ago by
Ram
44k • written 2.8 years ago by
Shred
★ 1.4k
0
votes
0
replies
103
views
Subset of Transcripts- How do I proceed with it?
Stringtie
updated 2 hours ago by
Ram
44k • written 1 day ago by
Varsha
• 0
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 1 day ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
250
views
Tools for chromosomal aneuploidy detection
human-genetics
aneuploidy
NGS
updated 2 hours ago by
Ram
44k • written 5 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
87
views
PyRMD
machine-learning
cheminformatics
Virtual-Screening
updated 40 minutes ago by
Ram
44k • written 1 day ago by
s
• 0
3
votes
4
replies
230
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
0
votes
0
replies
107
views
Determining rs ids from SNP HGV base ID?
rsID
HGV
SNP
updated 17 hours ago by
Ram
44k • written 1 day ago by
Katherine
• 0
0
votes
4
replies
306
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 5 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Sara
▴ 30
0
votes
1
reply
186
views
Facing problem with single cell rna seq annotation using singleR
singleR
scRNAseq
updated 50 minutes ago by
Ram
44k • written 2 days ago by
sc_analysis
• 0
0
votes
0
replies
96
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
1 day ago by
kl
▴ 10
0
votes
0
replies
110
views
Tubemap multiseq
vg
2 days ago by
karciharun42
• 0
5
votes
3
replies
5.9k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 2 days ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
0
votes
0
replies
123
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
Genotype-Likelihoods
Low-Coverage
Population-Genomics
ANGSD
updated 17 hours ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
241
views
How to decrease the motif score?
Motif-score
updated 40 minutes ago by
Ram
44k • written 3 days ago by
Hadia
• 0
0
votes
0
replies
148
views
immuCell Abundance infiltrate
ImmuCell
updated 40 minutes ago by
Ram
44k • written 3 days ago by
elbakri.fatimazahrae
• 0
1
vote
2
replies
249
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 2 days ago by
LauferVA
4.2k • written 3 days ago by
carolofharvest
▴ 40
168 results • Page
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Recent Votes
when I use htslib to write a bam. Error of "truncated file" shows by samtools
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
vg call - Selecting reference path to call on
Answer: vg call - Selecting reference path to call on
Comment: dbNSFP4.7a database format to Annovar Format?
Comment: dbNSFP4.7a database format to Annovar Format?
Comment: Is there any minimum number of counts in scRNAseq to consider that a gene is exp
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Recent Replies
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
Comment: coding and non-coding region of the viral genome
by
Ghada
• 0
As far I understand non coding region equal to the intergenic region? please can you write an example for how to calculate one region ? I…
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
Pierre Lindenbaum
162k
Thanks for the code, it's interesting. It doesn't solve the problem , but the code is missing `#include <htslib/bgzf.h>` and I cannot fin…
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Zhenyu Zhang
★ 1.2k
In the GDC, there are raw float value CNV data, and integer CNV values after advanced modeling. If you only want those floating-point numbe…
Comment: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
by
Ram
44k
Please edit your original post and add this at the top so everyone reads that first. GeneCards politely asks people not to scrape - not res…
Comment: I cannot download VG in any way
by
Ram
44k
In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg. Maybe this is the SequenceTube that OP…
Comment: I cannot download VG in any way
by
GenoMax
142k
I read that to mean that the only way they were able to download `vg` was by using `conda`. Since `SequenceTube` (whatever that is) require…
Comment: I cannot download VG in any way
by
Ram
44k
> The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube You're mentioning t…
Comment: I cannot download VG in any way
by
Ram
44k
Also, OP buries the lede and uses a misleading title. They are able to install vg using conda, but that is secondary to them using a differ…
Comment: Can I count UMI-barcode combination without mapping?
by
GenoMax
142k
You can use some code I have here for inspiration: https://www.biostars.org/p/270737/#270753 You can extract the UMI by using. $ awk…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 540
I think 10 rounds in excessive. I usually only run 1-3 rounds (as long-read accuracy has improved I have used fewer and fewer rounds), but …
Comment: I cannot download VG in any way
by
GenoMax
142k
Why are you not downloading the `vg` binaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0 Use the `Click here to Downl…
Comment: Best practices in Fungal Genome Assembly
by
Umer
▴ 50
Hi, Thanks for your suggestions. > polish the long-read assembly afterwards Previously, I used Pilon for polishing and i did 10 rounds. (…
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
Jack
• 0
I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates. Repeats range from polyG tracts around 9-20…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 540
For the short-read strains: <br/> I would recommend just using SPADES For the strains with long-reads: <br/> I think spades and masurca as…
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