Latest
News
Jobs
Tutorials
Forum
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
90,510 results • Page
1 of 1811
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
73
views
Job:
Bioinformatician/Programmer at the University of Pennsylvania
pipelines
programmer
bioinformatician
python
r
51 minutes ago by
adamnaj
• 0
0
votes
0
replies
40
views
Job:
Bioinformatician at Turbine / Hungary
proteomics
cancerreserach
singlecell
python
r
53 minutes ago by
timea.volenter
• 0
0
votes
0
replies
9
views
panel of normals for mutect2
mutect2
gatk
NGS
PoN
somatic
1 hour ago by
lait
▴ 160
0
votes
0
replies
15
views
Understanding the ColData Matrix
RNA-SEQ
R
Micheal_Love
DESEQ2
2 hours ago by
raisamathenge
▴ 10
0
votes
1
reply
27
views
format conversion using OpenBabel
software
updated 2 hours ago by
Mensur Dlakic
★ 10k • written 3 hours ago by
roybatty269
• 0
0
votes
0
replies
19
views
How to compare enrichment scores?
enrichment
scores
3 hours ago by
fpizzagalli
• 0
580
votes
155
replies
64k
views
89 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
tutorial
training
News
updated 6 days ago by
Biostar
10 • written 4.4 years ago by
Istvan Albert
87k
0
votes
0
replies
19
views
Should I take FDR < 0.2 for differentially abundant bacteria found in meta-analysis random effect ?
FDR
Microbiome
3 hours ago by
deep771992chanda
▴ 30
0
votes
1
reply
45
views
Program for predicting RNA sequences that may bind to a protein Domain
protein
Binding
domain
RNA
updated 3 hours ago by
Mensur Dlakic
★ 10k • written 7 hours ago by
noahhelton98
▴ 10
2
votes
5
replies
246
views
Understanding TCGA's ASCAT copy number data
tcga
ascat
copy number
updated 4 hours ago by
Zhenyu Zhang
▴ 270 • written 6 weeks ago by
loughrae
▴ 70
0
votes
1
reply
87
views
GDC Data Query
RNA-Seq
updated 4 hours ago by
Zhenyu Zhang
▴ 270 • written 29 days ago by
p20170409
• 0
1
vote
3
replies
57
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo
transcriptome
redundancy-reduction
updated 5 hours ago by
GenoMax
99k • written 5 hours ago by
Dunois
▴ 620
0
votes
5
replies
109
views
Cellranger count.srun issues
cellranger
srun
updated 5 hours ago by
GenoMax
99k • written 7 hours ago by
gonzalezb549
• 0
1
vote
1
reply
82
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS
power
updated 7 hours ago by
Kevin Blighe
72k • written 4 days ago by
moxu
▴ 480
1
vote
1
reply
2.0k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
updated 7 hours ago by
Kevin Blighe
72k • written 1 day ago by
leesooyeon94
▴ 10
0
votes
1
reply
58
views
Contradiction in Harzard ratio and Log fold change
Foldchange
Cancer
HR
HarzardRatio
LogFC
updated 7 hours ago by
Kevin Blighe
72k • written 1 day ago by
Mran
• 0
0
votes
0
replies
36
views
Refs/tools for protein interactomes
Protein
PSI-MI
Interactome
Orthologs
PPI
6 hours ago by
ian.will
• 0
0
votes
3
replies
95
views
How to plot a image like this.
plot
Bioinformatics
Cancer
R
Genome
updated 8 hours ago by
galen.seilis
• 0 • written 9 hours ago by
lincaijin1994
• 0
1
vote
2
replies
87
views
HaplotypeCaller VCF depth is greater than the number of reads in bam
HaplotypeCaller
vcf
gatk
4 hours ago by
wang.yiguan
• 0
0
votes
1
reply
52
views
How to get Data from https://www.orthodb.org/ by the list of UniprotID
Bioinformatics
updated 9 hours ago by
GenoMax
99k • written 16 hours ago by
Trinh
• 0
1
vote
4
replies
86
views
samtools idxstats unplaced contigs
contig
STAR
samtools
updated 9 hours ago by
Martombo
★ 2.7k • written 11 hours ago by
LacquerHed
• 0
0
votes
2
replies
62
views
16S data classification using kraken and centrifuge
centrifuge
16S
classification
kraken
updated 8 hours ago by
cpad0112
15k • written 10 hours ago by
twinklemishra0892
• 0
0
votes
3
replies
87
views
Differential expression analysis with LIMMA results
DGE
2 hours ago by
najioumayma
▴ 10
0
votes
1
reply
50
views
Is there a way to include not conda package/programs to snakemake environment?
Non-Conda_packages
Snakemake
updated 9 hours ago by
Arup Ghosh
2.8k • written 11 hours ago by
lmlukoseviciute
▴ 20
1
vote
1
reply
49
views
How to download all the Zn-binding protein sequences from MetalPDB?
PDB
NCBI
protein
python
database
updated 11 hours ago by
GenoMax
99k • written 11 hours ago by
Kumar
▴ 50
0
votes
0
replies
26
views
How to assemble short DNA sequences using ABYSS?
sequence
multiple-alignment
assembly
11 hours ago by
anikcropscience
▴ 40
0
votes
1
reply
44
views
How to run SPAdes assembler with bam files?
spades
assembler
bam
updated 11 hours ago by
GenoMax
99k • written 12 hours ago by
marongiu.luigi
▴ 560
2
votes
1
reply
55
views
Filter contig fasta file by GC content
contig
gc
updated 12 hours ago by
GenoMax
99k • written 12 hours ago by
victoriahristovaa
• 0
0
votes
0
replies
22
views
Why were all TCGA SVS slides redacted?
slides
slide
tcga
svs
digital
12 hours ago by
ceruleanivy
▴ 30
0
votes
0
replies
25
views
DisGeNET plugin usage error
DisGeNET
phenotype
plugin
vep
11 hours ago by
enes
• 0
0
votes
0
replies
19
views
negative BAF values OH
LOH
cnvkit
BAF
12 hours ago by
John
• 0
0
votes
2
replies
84
views
MASURCA output
masurca
13 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
39
views
Job:
Research assistant in straining engineering at DTU Center of Biosustainability
engineering
coli
Biofoundry
E.
Strain
14 hours ago by
info
▴ 60
0
votes
0
replies
34
views
Job:
Research assistant for yeast natural products project at DTU Biosustain
yeast
preps
DNA
DTU
Biosustain
CRISPR
15 hours ago by
info
▴ 60
1
vote
8
replies
143
views
how to select peaks at not transcribed genes
bedtools
transcribed
peaks
not_trasncribed
updated 11 hours ago by
ATpoint
48k • written 15 hours ago by
Lila M
▴ 910
0
votes
0
replies
32
views
Job:
Analytical chemist (RA) for yeast natural products project at DTU Biosustain
HPLC
yeast
biochemistry
15 hours ago by
info
▴ 60
9
votes
8
replies
135
views
How to combine 2 incomplete GTF
Cufflinks
Cuffcompare
GTF
Cuffmerge
Merge
12 hours ago by
rafaelsolersanblas
▴ 70
5
votes
3
replies
175
views
R command worked yesterday, but stalls today?
R
updated 10 hours ago by
Ram
32k • written 1 day ago by
cthangav
• 0
0
votes
4
replies
150
views
Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work
bwa-mem2
conda
snakemake
pipeline
14 hours ago by
aka
• 0
3
votes
3
replies
91
views
Extract chromosome 1 - 22 fasta file
fasta
updated 18 hours ago by
shenwei356
5.8k • written 18 hours ago by
shubhamkumbhar420
• 0
0
votes
1
reply
71
views
GATK GenomicsDBImport for consolidate GVCF
GATK
GenomicsDBImport
consolidate
updated 18 hours ago by
Pierre Lindenbaum
135k • written 19 hours ago by
mscpythonstudy
• 0
0
votes
1
reply
87
views
Question about methods monitoring the change from dsDNA/RNA to ssRNA/DNA
RNA
DNA
chaser
Substrate
updated 17 hours ago by
ATpoint
48k • written 20 hours ago by
1063625819
• 0
0
votes
1
reply
88
views
SHAPEIT2 - ERROR "BAD RECOMBINATION RATE"
shapeit2
phasing
updated 17 hours ago by
4galaxy77
▴ 400 • written 21 hours ago by
GiantSilverSoy
▴ 20
0
votes
0
replies
78
views
How to download pedigree (SNP's) from cattle
pedigree
data
snp
inference
haplotype
22 hours ago by
S. Roa
• 0
0
votes
0
replies
61
views
Job:
Multiple data scientist positions in computational biomedicine
CompBiology
Bioinformatics
MachineLearning
23 hours ago by
pandey.gaurav
▴ 130
4
votes
5
replies
151
views
GSEA for RNA_seq dataset
DEGs
GSEA
RNA_seq
updated 14 hours ago by
ATpoint
48k • written 1 day ago by
1961012
• 0
0
votes
0
replies
33
views
OMA output document error
OMA
output
document
error
1 day ago by
Yong
• 0
4
votes
4
replies
115
views
Hunting invisible characters?
adaptor
adapter
grep
updated 1 day ago by
seidel
7.6k • written 1 day ago by
geneticatt
▴ 120
0
votes
0
replies
46
views
Alternative Refence Allele in PLINK2 data files
PLINK2
ALLELE
1 day ago by
carlstat123
• 0
2
votes
4
replies
163
views
How can I Extract Transposable element from a new genome assembly?
genome
transposons
assembly
annotations
10 hours ago by
jaqx008
▴ 90
90,510 results • Page
1 of 1811
Recent Votes
Answer: HaplotypeCaller VCF depth is greater than the number of reads in bam
Answer: CNVkit detected CNV number
A: CNVkit : small CNV calling
A: CNVkit : small CNV calling
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
Comment: Redundancy reduction of de novo transcriptome assemblies with Compacta?
A: Extract Sub-Set Of Regions From Vcf File
Recent Locations •
All
Jinan,
1 minute ago
Japan,
4 minutes ago
Ireland, Republic of,
8 minutes ago
United States,
17 minutes ago
Beijing,
18 minutes ago
New York,
19 minutes ago
United States,
21 minutes ago
Recent Awards •
All
Popular Question
to
I0110
▴ 120
Teacher
to
Alex Reynolds
32k
Popular Question
to
ivivek_ngs
★ 5.1k
Voter
to
Leandro Lima
▴ 960
Popular Question
to
ATCG
▴ 300
Popular Question
to
jimhavrilla
▴ 10
Popular Question
to
morteza.mahmoudisaber
▴ 80
Recent Replies
Answer: format conversion using OpenBabel
by
Mensur Dlakic
★ 10k
It says clearly on their [**web page**][1] that `sdf` and `pdbqt` are among supported formats. If you can't do it directly, try converting …
Answer: Program for predicting RNA sequences that may bind to a protein Domain
by
Mensur Dlakic
★ 10k
I don't think you will be able to find such a tool. To answer your question more broadly, we do not have the ability to predict target sequ…
Comment: HaplotypeCaller VCF depth is greater than the number of reads in bam
by
wang.yiguan
• 0
Thanks, `--dont-use-soft-clipped-bases` solved the problem. It seems `samtools view/tview` doesn't show the soft clip base. If I don't u…
Answer: Understanding TCGA's ASCAT copy number data
by
Zhenyu Zhang
▴ 270
TCGA SNP6 ASCAT data shares the same format as WGS ASCAT data. If you search ASCAT in GDC documentation, you will find this page with det…
Answer: GDC Data Query
by
Zhenyu Zhang
▴ 270
are you complaining about getting full matrix data instead of truncated data? btw, for TCGA data in GDC, better to specify if it's legacy …
Comment: Meaning letters in TCGA sample barcode field
by
Zhenyu Zhang
▴ 270
I am pretty sure CPT is from CPTAC, and HCM is from HCMI. Neither are TCGA projects. Btw, using barcode is not a good habit in general. I …
Comment: Identification of the sequence insertion site in the genome
by
LacquerHed
• 0
If the BAM file represents a pretty small insertion, how can it be found once opened in IGV? Thanks.
Comment: Redundancy reduction of de novo transcriptome assemblies with Compacta?
by
GenoMax
99k
You can try it out and let us know :-) Good to know about it though. Thanks for posting the link.
Comment: Redundancy reduction of de novo transcriptome assemblies with Compacta?
by
Dunois
▴ 620
Hi @genomax , how are you? I'm looking at `Compacta` because I'd rather not use `CD-HIT` or `MMseqs2` if I can.
Comment: Redundancy reduction of de novo transcriptome assemblies with Compacta?
by
GenoMax
99k
Have you tried `CD-HIT` ([**LINK**][1]) for this application? [1]: http://weizhongli-lab.org/cd-hit/
Comment: Cellranger count.srun issues
by
GenoMax
99k
That does not make logical sense based on error which said command not found. If a prior script worked with same `PATH` but if this is gene…
Comment: Cellranger count.srun issues
by
gonzalezb549
• 0
cellranger is for sure installed. A sample script using the same commands just different fastq paths worked fine but for some reason this s…
Comment: Cellranger count.srun issues
by
gonzalezb549
• 0
The path used has worked on previous scripts but I tried what you said. It still resulted in the same error.
Comment: Which Fasta file and GTF file to use in STAR alignment
by
opplatek
▴ 110
You don't have to change the default `--sjdbOverhang` value unless you have very short reads (less than 50 bp; see [here][1]). If your read…
Comment: Cellranger count.srun issues
by
GenoMax
99k
> cellranger: command not found. Are you sure this `PATH` value is correct `/network/rit/misc/scratch/single_cell/cellranger/cellranger=3.…
Traffic: 1116 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6