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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
3
views
phylip format sequence name/header issue
phylogentics
6 minutes ago by
hafiz.talhamalik
▴ 340
0
votes
0
replies
4
views
Questions on file nomenclature in JGI Genome Portal for BUSCO analysis
BUSCO
annotation
JGI
just now by
Zeng Hao
• 0
0
votes
0
replies
5
views
Difficulty returning appropriate info. with esearch and/or efetch
esearch
dbsnp
efetch
31 minutes ago by
Vincent Laufer
★ 2.2k
0
votes
0
replies
14
views
Time course RNA-seq
R
edgeR
GEO
1 hour ago by
ShowPow
▴ 20
0
votes
0
replies
13
views
Does PCAWG have any advantage compared to TCGA for studying protein-coding regions?
TCGA
PCAWG
1 hour ago by
Zahra
▴ 60
0
votes
1
reply
43
views
Difference between clusterProfiler and gProfileR
clusterProfiler
scRNA-seq
GO
gProfileR
KEGG
updated 2 hours ago by
Arup Ghosh
3.0k • written 6 hours ago by
Zqall
• 0
0
votes
1
reply
52
views
SNV, CNA, SV
SV
CNA
SNV
updated 35 minutes ago by
Vincent Laufer
★ 2.2k • written 12 hours ago by
Bogdan
★ 1.3k
3
votes
2
replies
195
views
download just a chromosome from SRA toolkit
toolkit
SRP
linux
bioinformatics
updated 15 hours ago by
ATpoint
64k • written 2 days ago by
amahdi779
• 0
11
votes
19
replies
4.7k
views
9 follow
Extract sequences from a list of ID
software error
sequence
updated 12 hours ago by
GenoMax
119k • written 21 months ago by
doinelpierrot
▴ 30
689
votes
160
replies
93k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
960 • written 5.7 years ago by
Istvan Albert
94k
1
vote
1
reply
85
views
Convert mpileup file into dataframe
variantcalling
bcftools
samtools
updated 17 hours ago by
ATpoint
64k • written 18 hours ago by
kirillkirilenko.tomsk
• 0
0
votes
0
replies
50
views
annovar DB download problem (hg38)
annovar
intevar
updated 2 hours ago by
Arup Ghosh
3.0k • written 18 hours ago by
Chang Ki
• 0
0
votes
0
replies
50
views
GBS data analysis
gbs
SNP
sequencing
analysis
genotyping
20 hours ago by
girishkumarashwini
• 0
1
vote
2
replies
105
views
Order of Normalization/Surrogate variable analysis(or even known batch correction)/QC
Normalization
Batch
QC
correction
effect
20 hours ago by
english.server
▴ 280
0
votes
1
reply
73
views
Build a Signature Matrix File from Single-Cell RNA Sequencing Data
CIBERSORTx
updated 23 hours ago by
Kevin Blighe
82k • written 1 day ago by
QP
• 0
0
votes
2
replies
104
views
Why weblogo of biopython doesn't work?
Bioinformatics
Weblogo
Biopython
1 hour ago by
Plus
• 0
0
votes
0
replies
77
views
Control detected variants for normal samples in dragen
calling
illumina
variants
dragen
alignment
1 day ago by
Nemo
• 0
0
votes
0
replies
109
views
Error in Create switchAnalyzeRlist
Genome
annotation
updated 1 day ago by
rpolicastro
9.4k • written 1 day ago by
Saeed
• 0
1
vote
2
replies
190
views
Why different read depth on IGV and in VCF for a variant
depth
GATK
read
haplotypecaller
IGV
1 day ago by
pragnapcu
• 0
1
vote
1
reply
136
views
Setting cut-off value
bioinformatics
cutoff
R
ngs
tradis
updated 21 hours ago by
ATpoint
64k • written 1 day ago by
jennakrishnamurthy
• 0
2
votes
3
replies
203
views
Can IGV simultaneously show alignments for different reference genomes in different panes?
IGV
alignments
visualization
10 hours ago by
appropiate
▴ 40
2
votes
3
replies
205
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
updated 14 hours ago by
manaswwm
▴ 260 • written 1 day ago by
JACKY
▴ 10
0
votes
2
replies
152
views
Does Cellranger filter out doublet?
cellranger
scRNA
1 day ago by
Emily
▴ 20
0
votes
0
replies
89
views
Questions regarding iupac2meme and to investigate a DNA sequence for TFBS
MEME
Suite
1 day ago by
Placeholder@12654926
• 0
1
vote
4
replies
198
views
How to insert dbSNP in a database?
dbsnp
database
1 day ago by
magnolia
• 0
0
votes
2
replies
2.3k
views
MAKER AED score
MAKER
AED-score
RNA-Seq
EVM
annotation
updated 1 day ago by
lei
• 0 • written 5.0 years ago by
Tye Kahn
▴ 20
0
votes
3
replies
707
views
Spatial transcriptomics without the h5 file
data
spatial
single
transcriptomics
h5
updated 1 day ago by
swainkasish
• 0 • written 7 months ago by
jordi.diaz-manera
▴ 10
0
votes
3
replies
226
views
searching for information in a file and saving to another- sequence access code
python
phylogenetic
tree
excel
sequence
updated 2 days ago by
Mensur Dlakic
★ 20k • written 2 days ago by
Alexandra
• 0
3
votes
4
replies
348
views
Has anybody managed to install and run GroopM lately?
metagenomics
groopM
binning
updated 2 days ago by
v.berriosfarias
▴ 60 • written 4 days ago by
JohnVollmers
▴ 10
0
votes
0
replies
140
views
Comparing two CUT&RUN (similar to ChipSeq) generated peaks
chipseq
peak
cnr
heatmap
deeptools
call
2 days ago by
susan.kuo.run
• 0
0
votes
4
replies
294
views
Warning - longer object length is not a multiple of shorter object length
genelength
r
TPM
RNA-seq
1 day ago by
JACKY
▴ 10
3
votes
6
replies
293
views
Expanding reference genome with alt loci and decoy sequences
read
alt
reference
decoy
genome
alignment
1 day ago by
appropiate
▴ 40
0
votes
3
replies
251
views
Centrally installed Braker2 error: AUGUSTUS_CONFIG_PATH/species is not writeable.
braker2
augustus
updated 1 day ago by
Michael Dondrup
52k • written 2 days ago by
Timotheus
▴ 10
2
votes
1
reply
148
views
fgsea
permutations
fgsea
updated 2 days ago by
LChart
▴ 600 • written 2 days ago by
Mary
• 0
0
votes
0
replies
119
views
CWL and Arvados
CWL
workflow
manager
2 days ago by
Bogdan
★ 1.3k
1
vote
1
reply
416
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
Correlation
DESeq
RNAseq
updated 2 days ago by
LChart
▴ 600 • written 2 days ago by
keshav.prasad.gubbi
• 0
2
votes
2
replies
152
views
List of cyanobacterial refseq genomes
cyanobacteria
refseq
2 days ago by
Sam Wheeler
• 0
2
votes
1
reply
160
views
Plink : Variant names are limited to 16000 characters
plink
vcftools
Varient
GWAS
bcftools
updated 2 days ago by
chrchang523
9.5k • written 3 days ago by
skjobs0123
▴ 190
0
votes
2
replies
212
views
Error in MuscleCommandline (biopython)
Bioinformatics
Biopython
MultipleSequenceAlignment
Python
2 days ago by
Plus
• 0
0
votes
0
replies
107
views
ChIPQC Error
ChIP-seq
ChIPQC
2 days ago by
tsomakiank
• 0
74
votes
21
replies
10k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
enrichment
microarray
Tutorial
GSEA
RNA-Seq
updated 2 days ago by
Aadil Rashid
• 0 • written 22 months ago by
Hamid Ghaedi
★ 2.6k
1
vote
3
replies
260
views
DEXSeq Error loading in data set - subscript out of bound
DEXSeq
Exon
RNA-Seq
Expression
Count
2 days ago by
osiemen
▴ 20
0
votes
0
replies
118
views
What Is The Best Method To Find Orthologous Genes Of One Species And Compare With Another Species?
genes
tools
ortholog
database
2 days ago by
merimi
▴ 20
0
votes
0
replies
114
views
Eggnog mapper -> Blast2Go for Gene Ontology??
blast2go
eggnog
mapper
GO
2 days ago by
Megan
• 0
0
votes
1
reply
132
views
How to get results from a curl
Ensembl
Biomart
Uniprot
updated 2 days ago by
Matthias Zepper
★ 1.5k • written 2 days ago by
Recep
• 0
3
votes
3
replies
200
views
transcription binding site prediction from fasta sequence
transcription
site
jaspar
updated 2 days ago by
ATpoint
64k • written 2 days ago by
newbio
• 0
0
votes
3
replies
182
views
How to convert Uniprot IDs to Ensemble Gene IDs
Ensembl
Biomart
Uniprot
updated 2 days ago by
GenoMax
119k • written 2 days ago by
Recep
• 0
2
votes
1
reply
156
views
Compare 2 sets of genes
genes
python
compare
Repair
R
Recombination
Homologous
updated 2 days ago by
grant.hovhannisyan
★ 2.4k • written 2 days ago by
Alon
▴ 10
6
votes
5
replies
264
views
Why do I have sequential 100 G (GGGGGGGGGG...) in R2 FastQC report?
FastQC
updated 1 day ago by
Arup Ghosh
3.0k • written 2 days ago by
Giulia.cosenza
▴ 70
1
vote
0
replies
124
views
Strand orientation and GC skew
strand
skew
CGView
orientation
CG
2 days ago by
A_heath
▴ 90
1,000 results • Page
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Why the result of GSEA and ssGSEA is different?
4-group RNAseq experiment- GSEA vs ssGSEA?
Are upset plots bad for differential expression analysis?
Answer: Are upset plots bad for differential expression analysis?
Answer: extracting sequences from a bam file
A: Best Genome Assembler and Genome Annotation tools and pipelines
Top/best RNAseq workflow including anlaysis results for function annotation
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Recent Replies
Comment: SNV, CNA, SV
by
Vincent Laufer
★ 2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work?
by
Plus
• 0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR
by
Arup Ghosh
3.0k
> The GO terms output by gprofileR are generally quite similar to those > output by clusterProfiler, but there are small differences due to…
Comment: hgmd variants from Ensembl
by
Sanjar
▴ 140
Did you figure out how to do this?
Comment: Why weblogo of biopython doesn't work?
by
Arup Ghosh
3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
appropiate
▴ 40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID
by
GenoMax
119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes?
by
manaswwm
▴ 260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
cmdcolin
★ 2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit
by
ATpoint
64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit
by
shelkmike
▴ 660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID
by
Neel
▴ 20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated [WARN] symbol ">" detected…
Answer: Convert mpileup file into dataframe
by
ATpoint
64k
No, don't do any custom data fiddling. Follow the manual of bcftools for variant calling, it covers all you need: https://samtools.github.i…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
GenoMax
119k
You can open multiple instances of IGV and display multiple genome alignments.
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴ 10
Thanks for the headsup about the positive control! Any way I can add another pair of reads to the bam file, containing my positive control …
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