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108,010 results • Page
1 of 2161
Sort: Rank
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Votes
Replies
0
votes
0
replies
24
views
Problem with tximport and plasmodium falciparum
tximport
2 hours ago by
bioinfo
▴ 20
2
votes
3
replies
81
views
How to map and annotate gene symbols to gene type?
Ensembl
RefSeq
UCSC
biomart
RNA-Seq
updated 2 hours ago by
GenoMax
125k • written 4 hours ago by
mohammedtoufiq91
▴ 170
716
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
0
votes
0
replies
27
views
Stringtie prepDE.py script
input
deseq2
gene
counts
count
matrix
3 hours ago by
Aiswarya
• 0
0
votes
1
reply
43
views
BLAST reference genome indexing
blastn
fasta
shell
updated 3 hours ago by
GenoMax
125k • written 3 hours ago by
bhumm
▴ 20
0
votes
0
replies
25
views
Averaging across multiple proteomic experiments
statistics
proteomics
R
3 hours ago by
bhumm
▴ 20
0
votes
0
replies
39
views
Copy Number Variants, where to start?
CNV
annotation
4 hours ago by
paolo
▴ 60
4
votes
6
replies
263
views
command line - how to change name of multiple files at the same time
bash
line
command
script
updated 5 hours ago by
shenwei356
7.8k • written 22 hours ago by
tiziana
• 0
0
votes
1
reply
1.3k
views
rDGIdb - VCF input error using locateVariant command (VariantAnnotation)
genome
sequence
updated 5 hours ago by
Gaurav
• 0 • written 3.2 years ago by
tarapcsakszabolcs
• 0
0
votes
0
replies
45
views
mosdepth coverage & transcripts per million
TPM
coverage
metagenome
mosdepth
6 hours ago by
hannahf
• 0
0
votes
0
replies
46
views
FATAL: While performing build: build image size <= 0 - Issues With Singularity
R
Docker
Singularity
7 hours ago by
Indira
• 0
0
votes
1
reply
67
views
Methods for downsampling coverage in a VCF
BCFTools
downsampling
WGS
sequencing
GATK
updated 6 hours ago by
Medhat
9.5k • written 7 hours ago by
a
• 0
0
votes
5
replies
274
views
Error: ##fileformat=VCFv4.2 does not exist
Pharmcat
VCF
updated 7 hours ago by
sbstevenlee
▴ 480 • written 1 day ago by
taniamahmood38
▴ 20
0
votes
1
reply
73
views
Extract species-specific SNPs from VCF files
SNPs
vcf
tools
updated 8 hours ago by
cfos4698
▴ 570 • written 9 hours ago by
RT
▴ 370
0
votes
0
replies
57
views
exchange the monocle data with Seurat
monocle3
Seurat
8 hours ago by
alghezim1
• 0
0
votes
0
replies
56
views
docker build Command Works Yet It Does Not Create A Docker Container
Linux
build
R
docker
8 hours ago by
Indira
• 0
0
votes
0
replies
49
views
Questions about HVGs and HEGs in single cell research
single-cell
machine-learning
updated 7 hours ago by
Ram
38k • written 8 hours ago by
me
• 0
0
votes
0
replies
55
views
average expression function and pct
seurat
average
pct
expression
and
9 hours ago by
rasing02
• 0
0
votes
0
replies
74
views
Is there a way to run docker on an R Markdown from Linux command line?
Docker
R
Markdown
9 hours ago by
Indira
• 0
0
votes
0
replies
57
views
GoSemSIm - function mgeneSim() is resulting in similarity matrix without 1s od diagonal
vs
Gosim
GoSemSIm
10 hours ago by
eliska.ochodkova
• 0
0
votes
2
replies
126
views
Database with gene family annotations
RNA-seq
database
10 hours ago by
kjs22
• 0
0
votes
2
replies
132
views
Error with FindConservedMarkers()
FindConservedMarkers
11 hours ago by
Chris
▴ 60
0
votes
3
replies
187
views
comparing two metagenomics data sets
metagenomics
updated 12 hours ago by
Mensur Dlakic
★ 22k • written 19 hours ago by
arshad1292
▴ 80
1
vote
2
replies
114
views
Can't view the last rows
scRNA-Seq
updated 12 hours ago by
brunobsouzaa
▴ 800 • written 12 hours ago by
Chris
▴ 60
1
vote
4
replies
247
views
General approach for unsupervised clustering of bulk RNAseq samples and deriving/applying gene signature
clustering
RNAseq
DESeq2
updated 14 hours ago by
Spirogyra
• 0 • written 19 hours ago by
Matthias
▴ 70
0
votes
0
replies
67
views
Extract differen variants of a vcf file comparing to vcf files
gatk
bedtools
mutect2
vcftools
variant
updated 12 hours ago by
GenoMax
125k • written 14 hours ago by
minoo
▴ 10
1
vote
2
replies
137
views
make BED file from existing BIM and FAM files
plink
updated 13 hours ago by
chrchang523
10.0k • written 18 hours ago by
josephine.henry
• 0
0
votes
3
replies
167
views
BWA-mem not working with Snakemake + singularity
snakemake
bwa
singularity
updated 12 hours ago by
Jeremy Leipzig
21k • written 15 hours ago by
brunobsouzaa
▴ 800
1
vote
2
replies
88
views
download a set of proteome from uniprot
uniprot
download
batch
14 hours ago by
Juke34
7.5k
1
vote
8
replies
1.7k
views
calctruequality in bbmap
Assembly
BBtools
calctruequality
q score
BBmap
updated 15 hours ago by
Andreas
★ 2.5k • written 4.7 years ago by
coyk
• 0
0
votes
1
reply
134
views
Tool to combine Germline Variant call from different variant callers
haplotypecaller
gatk
snps
updated 16 hours ago by
David Langenberger
9.8k • written 1 day ago by
rohitsatyam102
▴ 690
6
votes
4
replies
130
views
Equivalent to SeqMan alignment tool
SeqMan
alignments
15 hours ago by
A_heath
▴ 120
1
vote
9
replies
224
views
Subbmission Data
submission
in
RNA-seq
data
paper
updated 14 hours ago by
seidel
10k • written 18 hours ago by
GiV17
▴ 40
5
votes
8
replies
525
views
RNA Editing data from RNA-seq
Editing
RNA
updated 18 hours ago by
Juke34
7.5k • written 4 days ago by
Genetics
▴ 10
0
votes
1
reply
110
views
Visualization of Enrichment score for spatial 10x visium samples
visium
transctiptome
10x
enrichment
scores
spatial
updated 19 hours ago by
Nicolas Rosewick
10k • written 19 hours ago by
Omics data mining
▴ 210
0
votes
0
replies
58
views
News:
RNA-Seq Data Analysis Workshop - Join us in Berlin, Germany from March 27-30, 2023!
NGS
transcriptomics
workshop
20 hours ago by
David Langenberger
9.8k
0
votes
6
replies
198
views
Issue in import files in Metaboanalyst
file
import
vector
Metaboanalyst
atomic
14 hours ago by
Andrea
▴ 10
0
votes
0
replies
80
views
database for better classification of illumina contigs
classification
illumina
contigs
NR
updated 19 hours ago by
GenoMax
125k • written 21 hours ago by
sapuizait
▴ 10
0
votes
2
replies
125
views
CNV Prediction Tools
NGS
Variant
CNV
Calling
updated 21 hours ago by
Lian
▴ 30 • written 23 hours ago by
adarsh_pp
▴ 10
0
votes
3
replies
173
views
How to unzip a file with .bgz extention
.bgz
unzip
updated 18 hours ago by
GenoMax
125k • written 22 hours ago by
taniamahmood38
▴ 20
0
votes
1
reply
235
views
Variant calling on synthesized DNA
Nanopore
Calling
MinION
Variant
sequencing
SNP
Python
updated 22 hours ago by
colindaven
4.4k • written 22 days ago by
stan.aanhane
▴ 30
0
votes
0
replies
93
views
FWS calculation using plink data
vcf
Fws
Plink
22 hours ago by
anithanagaraj93
• 0
0
votes
0
replies
102
views
qPCR missing data
Bioconductor
Analysis
Expression
qPCR
23 hours ago by
Prerna
• 0
0
votes
0
replies
83
views
imputing haplotypes from variants in a VCF file - vcfIndexFile
practical
graph
haplotype
vcf
imputation
PHG
1 day ago by
matt.shenton
▴ 40
0
votes
0
replies
88
views
Pathway Analysis for Cancer Spatial Transcriptomics Characterization
Spatial
Pathway
Oncology
Transcriptomics
Enrichment
updated 16 hours ago by
GenoMax
125k • written 1 day ago by
Flemming
• 0
1
vote
1
reply
129
views
difference between chip-seq and association study
association
chip-seq
TWAS
updated 1 day ago by
seidel
10k • written 1 day ago by
rheab1230
▴ 120
2
votes
3
replies
245
views
Issues With Using Singularity In Order To Run Software "quested access to the resource is denied"
Singularity
10 hours ago by
Indira
• 0
0
votes
6
replies
1.3k
views
Gene trans map for Trinotate input using non-Trinity assembled transcriptome?
RNAseq
transcriptomics
Trinotate
assembly
annotation
updated 1 day ago by
liyong
▴ 40 • written 12 months ago by
Corey
• 0
3
votes
5
replies
395
views
How to download all Gene Ontology (GO) IDs with their associated vocabulary?
download
GO
gene_ontology
1 day ago by
Jimmy
• 0
0
votes
1
reply
139
views
gff2bed fails with "Non-numeric start coordinate. "
bedops
updated 1 day ago by
Jimmy
• 0 • written 1 day ago by
scottbrainard
▴ 50
108,010 results • Page
1 of 2161
Recent Votes
Comment: How to map and annotate gene symbols to gene type?
Answer: command line - how to change name of multiple files at the same time
Answer: How to map and annotate gene symbols to gene type?
comparative proteomic analysis
How to compare two proteomes
Answer: RNA Editing data from RNA-seq
C: Sequence length from Fasta
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Comment: How to map and annotate gene symbols to gene type?
by
GenoMax
125k
Yes it should. Look for `biotypes` ([LINK][1]). [1]: https://www.ensembl.org/info/genome/genebuild/biotypes.html
Comment: How to map and annotate gene symbols to gene type?
by
mohammedtoufiq91
▴ 170
@genomax thank you. Does this works in `biomart` R package too?
Answer: How to map and annotate gene symbols to gene type?
by
GenoMax
125k
Use BioMart at [**Ensembl**][1]. Choose `Attributes` as needed. ![enter image description here][2] [1]: http://www.ensembl.org/in…
Answer: BLAST reference genome indexing
by
GenoMax
125k
`makeblastdb` is creating the index from `mydb.fsa` (which is your reference) file. This results in the set of files you name above. `mydb`…
Comment: pyCirclize - Circular visualization in Python
by
Jimmy
• 0
That was fast! Thanks!
Answer: command line - how to change name of multiple files at the same time
by
shenwei356
7.8k
Try [brename](https://github.com/shenwei356/brename), it's safe and powerful. also read this post: https://www.biostars.org/p/9487877/ …
Comment: batch renaming FASTQ files
by
shenwei356
7.8k
The `brename` version should be brename -p '^(\w+?)_.+([12]).fastq.gz$' -r '${1}_$2.fastq.gz'
Answer: rDGIdb - VCF input error using locateVariant command (VariantAnnotation)
by
Gaurav
• 0
I think the issue is that the `seqlevels `do not match. Apparently, one should be a subset of the other. You could try restricting only to …
Comment: Methods for downsampling coverage in a VCF
by
Medhat
9.5k
I do not know how you want to downsample vcf file,. However, to downsample reads, you can use `seqtk sample` https://github.com/lh3/seqtk …
Answer: Error: ##fileformat=VCFv4.2 does not exist
by
sbstevenlee
▴ 480
I would also recommend checking out a different star allele-calling tool named PyPGx (see [docs](https://pypgx.readthedocs.io/en/latest/rea…
Answer: command line - how to change name of multiple files at the same time
by
cfos4698
▴ 570
I prefer the `rename` tool. I think you might need to install it with either something like `apt` (ubuntu), or `conda` (Linux, Mac, Windows…
Answer: Extract species-specific SNPs from VCF files
by
cfos4698
▴ 570
If I'm interpreting you correctly, you want to compare the VCF files, ignore SNPs shared by two (or more) species, and instead retain only …
Comment: Issues With Using Singularity In Order To Run Software "quested access to the re
by
Indira
• 0
Thank you I realized that the mistake I made was by not making a docker image.
Comment: intersect VCF files
by
Ram
38k
Which ID and QUAL values do you pick for the output VCF record? That choice makes the difference.
Answer: Database with gene family annotations
by
Mensur Dlakic
★ 22k
> I've queried the Panther database, but unfortunately it does not return annotations for all of my genes. For any reasonably-sized quer…
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