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206 results • Page
3 of 5
Sort: Votes
Rank
Views
Votes
Replies
1
vote
3
replies
234
views
Fastqc loop
fastQC
r
RNA-seq
1 day ago by
camillab.
▴ 130
1
vote
3
replies
260
views
How to convert between UniRef50 to EC/enzyme number?
Uniref
conversion
uniprot
enzyme
updated 2 days ago by
Elisabeth Gasteiger
★ 2.2k • written 3 days ago by
O.rka
▴ 680
1
vote
5
replies
442
views
Idat raw data conversion
idat
updated 3 days ago by
Giulio Genovese
▴ 330 • written 5 days ago by
Zi
• 0
1
vote
2
replies
171
views
STAR error EXITING because of FATAL ERROR: failed reading from temporary file
STAR
RNA-seq
updated 1 day ago by
GenoMax
134k • written 1 day ago by
erik.burchard
▴ 20
1
vote
3
replies
242
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 1 day ago by
ATpoint
76k • written 9 days ago by
rkc5
• 0
1
vote
1
reply
134
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 1 day ago by
ATpoint
76k • written 1 day ago by
Smriti
• 0
1
vote
2
replies
560
views
Cellchat log fold change
scRNA-seq
Fold-change
LRinteraction
CCI
cellchat
updated 5 days ago by
Ram
40k • written 10 weeks ago by
miyeok
• 0
1
vote
0
replies
562
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
4 days ago by
shelkmike
▴ 970
1
vote
2
replies
415
views
Ranked fold changes for non-replicated data
expression
metagenomics
LogFC
fold-change
updated 5 days ago by
Ram
40k • written 18 months ago by
Tom
▴ 540
1
vote
6
replies
3.2k
views
Extracting sequence, not reads, by position from bam
sequence
updated 22 hours ago by
manu
• 0 • written 5.0 years ago by
geneware
▴ 10
1
vote
5
replies
419
views
For high quality Telomere to telomere assemblies, is short read polishing still necessary
genome
illumina
sequencing
nanopore
wgs
updated 5 days ago by
Buffo
★ 2.3k • written 6 days ago by
Mark
• 0
0
votes
0
replies
106
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 1 day ago by
Ram
40k • written 1 day ago by
AndrMod
• 0
0
votes
1
reply
365
views
installation of Snapgene tool in Ubuntu
snapgene
Ubuntu
updated 1 day ago by
Ram
40k • written 5 months ago by
Fizzah
▴ 30
0
votes
1
reply
287
views
how to determine n_cells_by_count
scanpy
updated 6 days ago by
yl759
▴ 40 • written 10 weeks ago by
dalibenam64
• 0
0
votes
0
replies
112
views
qtlseq oserror 38
qtlseq
6 days ago by
지헌
• 0
0
votes
2
replies
118
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 3 hours ago by
luffy
▴ 30 • written 19 hours ago by
_quantum_girl_
▴ 10
0
votes
7
replies
1.5k
views
what does "total read count" means in fastqc file. how does it helpful for analysis
fastqc
updated 1 day ago by
Ram
40k • written 23 months ago by
Fizzah
▴ 30
0
votes
1
reply
180
views
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
scRNA-seq
Seurat
updated 1 day ago by
Ram
40k • written 2 days ago by
Sara
▴ 230
0
votes
1
reply
141
views
vg rna pantranscriptome
rna
vg
updated 1 day ago by
Jordan M Eizenga
▴ 360 • written 1 day ago by
z
• 0
0
votes
3
replies
209
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 1 day ago by
Ram
40k • written 1 day ago by
Fizzah
▴ 30
0
votes
2
replies
296
views
Extract Divergence Times and Corresponding Node Numbers from a Time Tree
phylogeny
R
ape
phytools
phylogenetics
1 day ago by
Simone
• 0
0
votes
3
replies
186
views
Errors while trying to run Scenic
Scenic
updated 1 day ago by
GenoMax
134k • written 1 day ago by
Stavroula
• 0
0
votes
0
replies
189
views
External validation in bioinformatics analyses
External
validation
6 days ago by
Saeedeh Salehi
▴ 10
0
votes
3
replies
254
views
VDJ reconstitution from 3' 10x genomics platforms
VDJ
updated 1 day ago by
Ram
40k • written 2 days ago by
gal.dadi
• 0
0
votes
7
replies
614
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 1 day ago by
rfran010
▴ 790 • written 6 days ago by
pb11
▴ 10
0
votes
1
reply
137
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 1 day ago by
Jordan M Eizenga
▴ 360 • written 1 day ago by
cfourps
▴ 10
0
votes
6
replies
928
views
How to run delly with multi-threading mode?
SV
calling
delly
updated 1 day ago by
bio-jr
▴ 10 • written 8 months ago by
Xi
• 0
0
votes
1
reply
207
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
updated 6 days ago by
Ram
40k • written 6 days ago by
Xuhao
• 0
0
votes
3
replies
458
views
CNV calling
CNV
NGS
Variant-Calling
updated 1 day ago by
Zhenyu Zhang
▴ 970 • written 8 months ago by
adarsh_pp
▴ 30
0
votes
2
replies
542
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
updated 1 day ago by
AS-git
• 0 • written 5 months ago by
Shriyansh
• 0
0
votes
0
replies
24
views
News:
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sars-cov-2
spikePprotein
computationalApproach
escapeMutations
sequenceAanalysis
2 hours ago by
Prem
• 0
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 22 hours ago by
aishwarya
• 0 • written 5.2 years ago by
blooming.daisy333
▴ 110
0
votes
0
replies
1
view
News:
Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
single
RNA-Seq
scRNA-Seq
cell
workshop
just now by
David Langenberger
10k
0
votes
3
replies
1.2k
views
how to calculate BAF and LRR from VCF or BCF files?
SNP
BAF
LRR
Variation
1 hour ago by
xiaoguang
▴ 120
0
votes
0
replies
179
views
Job:
Biology Assistant Professor in Bioinformatics, Agnes Scott College, Atlanta, GA
assistant-professor
tenure-track
updated 6 days ago by
Ram
40k • written 6 days ago by
jkovacs
• 0
0
votes
1
reply
113
views
gffread outputs empty gtf file
gff
gffread
gtf
updated 18 hours ago by
inedraylig
▴ 20 • written 22 hours ago by
sumitra.20
• 0
0
votes
2
replies
86
views
How to find positions with higher depth relative to their surroundings
depth
python
samtools
updated 50 minutes ago by
xiaoguang
▴ 120 • written 7 hours ago by
hyperdx1
• 0
0
votes
0
replies
207
views
Job:
Research Scientist 5 – Bioinformatics and Computer Biology, Center for Dementia Research (CDR), Nathan Kline Institute for Psychiatric Research
Neuroscience
Biostatistics
updated 18 hours ago by
Ram
40k • written 18 hours ago by
cdrinfo
• 0
0
votes
0
replies
68
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 18 hours ago by
Ram
40k • written 22 hours ago by
Mark
• 0
0
votes
0
replies
74
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
updated 18 hours ago by
Ram
40k • written 23 hours ago by
Thomas
• 0
0
votes
1
reply
83
views
Prank checkpoint and restore?
prank
alignment
updated 17 hours ago by
Ram
40k • written 17 hours ago by
Pit
• 0
0
votes
2
replies
217
views
DESeqDataSetFromMatrix error
deseq
6 days ago by
oduduabasi.isaiah
• 0
0
votes
2
replies
179
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
17 hours ago by
JLee
• 0
0
votes
10
replies
298
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
16 hours ago by
Y
• 0
0
votes
3
replies
110
views
Importance of Data Structures for Bioinformatics?
structures
data
Industry
Bioinformatic
updated 4 minutes ago by
xiaoguang
▴ 120 • written 7 hours ago by
S
• 0
0
votes
2
replies
132
views
how to evaluate SNPs that are regulating same gene expression across multiple tissues
snp
GTEx
updated 15 hours ago by
LChart
3.3k • written 17 hours ago by
rheab1230
▴ 140
0
votes
11
replies
649
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
15 hours ago by
evmae
• 0
0
votes
1
reply
111
views
Identifying common DEGs among multiple datasets
R
DEG
updated 14 hours ago by
bk11
★ 1.2k • written 21 hours ago by
Shma
• 0
0
votes
9
replies
472
views
Large number of gaps at the beginning of alignments
clustal-omega
DNA
alignment
updated 6 days ago by
Ram
40k • written 6 days ago by
Pit
• 0
0
votes
0
replies
68
views
Chromosome bias on RNA-Seq differential gene expression analysis
bias
rna-seq
chromosome
12 hours ago by
blz
▴ 10
206 results • Page
3 of 5
Recent Votes
What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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xiaoguang
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Recent Replies
Answer: Importance of Data Structures for Bioinformatics?
by
xiaoguang
▴ 120
Bioinformatics is a cross-disciplinary research subject and learning anything is a plus for future participation in related jobs. But right…
Answer: How to find positions with higher depth relative to their surroundings
by
xiaoguang
▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files?
by
xiaoguang
▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data
by
Diana
• 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings
by
d-cameron
★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data?
by
luffy
▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq
by
Chris
▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics?
by
d-cameron
★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu
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dk0319
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Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
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I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
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3.7k
even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
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3.7k
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Answer: What is the difference between norm --multiallelics -any versus --atomize?
by
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40k
I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
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