Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
138 results • Page
1 of 3
Sort: Votes
Rank
Views
Votes
Replies
4
votes
2
replies
2.3k
views
Signal Distribution Charts
ChIP-Seq
next-gen
R
updated 4 days ago by
Ram
37k • written 7.7 years ago by
John
13k
4
votes
4
replies
698
views
Analysis of Nanopore cDNA sequencing data
alignment
nanopore
sequencing
minimap2
1 day ago by
Nico80
▴ 60
4
votes
10
replies
3.5k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 4 days ago by
Ram
37k • written 7.7 years ago by
David_emir
▴ 460
4
votes
8
replies
1.9k
views
Select only sequences that align with X% of a query during blastp search
sequence
blast
alignment
updated 4 days ago by
Ram
37k • written 7.7 years ago by
dago
★ 2.7k
4
votes
5
replies
203
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
error
BAM
Bowtie
updated 1 day ago by
GenoMax
125k • written 2 days ago by
luzglongoria
▴ 40
3
votes
6
replies
519
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
6 days ago by
TN
• 0
3
votes
5
replies
6.2k
views
Converting Vcftools output to R readable format
vcf
SNP
R
vcftools
updated 5 days ago by
Ram
37k • written 7.7 years ago by
pifferdavide
▴ 100
3
votes
1
reply
167
views
RNA seq analysis from the data file which received from company
RNA
editing
updated 4 days ago by
4galaxy77
2.6k • written 4 days ago by
Genetics
• 0
2
votes
4
replies
174
views
Calculate sequencing file size?
storage
data
sequencing
plan
management
updated 2 days ago by
GenoMax
125k • written 2 days ago by
Lluís R.
★ 1.2k
2
votes
3
replies
10k
views
converting maf to vcf
Exome
maf2vcf
updated 5 days ago by
Ram
37k • written 7.7 years ago by
ashishchahl
• 0
2
votes
3
replies
273
views
What should be control group for differential expression in single cell? either distant normal samples or primary tumors when analysing metastatic sa…
single-cell
transcriptomics
differential-expression
RNAseq
updated 4 days ago by
ATpoint
68k • written 4 days ago by
gorizwango
▴ 30
2
votes
1
reply
187
views
Ancestral sequence reconstruction at each node of a gene tree
tree
reconstruction
ancestral
gene
updated 5 days ago by
Jesse
▴ 450 • written 10 days ago by
biomonte
▴ 210
2
votes
3
replies
270
views
SALMON Index build Process Killed!
salmon
index
mapping
3 days ago by
Soumajit
▴ 30
2
votes
4
replies
234
views
Ensembl ID to Gene Symbol Converter
ensembl
Homo_sapiens
BioMart
biotools
updated 1 day ago by
GenoMax
125k • written 4 days ago by
GA
• 0
2
votes
1
reply
1.2k
views
pair wise differences of different populations
snp
updated 4 days ago by
Ram
37k • written 7.7 years ago by
drshahzadbhatti
• 0
2
votes
4
replies
326
views
Change sample ID in BAM file to cell barcode
bam
samtools
barcode
scrna
5 days ago by
martin.grasshoff
• 0
2
votes
1
reply
184
views
bgzip error 4
bgzip
error4
vcf
updated 20 hours ago by
Pierre Lindenbaum
152k • written 1 day ago by
yb
▴ 10
1
vote
7
replies
360
views
Segmentation Fault error when running salmon quant
mapping
rnaseq
samon
updated 6 days ago by
Medhat
9.5k • written 6 days ago by
Daniel
• 0
1
vote
0
replies
2.3k
views
Scoring matrix of 3 sequence alignment
sequencing
multiple-sequencing
updated 4 days ago by
Ram
37k • written 7.7 years ago by
mhasa006
▴ 70
1
vote
7
replies
246
views
Downloading NT chunks from NCBI and creating a BLAST database
nucleotide
blast
nt
blastn
database_update.pl
updated 1 day ago by
GenoMax
125k • written 3 days ago by
Vinícius
• 0
1
vote
1
reply
171
views
Tools for annotating predicted genes?
Bioninformatics
updated 4 days ago by
samuel.a.odonnell
▴ 450 • written 5 days ago by
zack.saud
▴ 50
1
vote
0
replies
102
views
Meta-analysis of rare variant SAIGE-GENE output for WGS data
meta-analysis
rare
SAIGE
variant
1 day ago by
tacrolimus
▴ 100
1
vote
6
replies
254
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
updated 10 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
Emoji
• 0
1
vote
2
replies
222
views
Matching IDs between 3+ files and specifying output using dictionaries in Python
Dictionaries
inforstatements
Matching
loops
Python
2 days ago by
Jennifer
• 0
1
vote
3
replies
209
views
difference between target sequencing technologies
capture
sequencing
hybrid
wes
updated 1 day ago by
GenoMax
125k • written 1 day ago by
pingu77
▴ 10
1
vote
5
replies
2.5k
views
who can give me the data of genome music bmr calc-covg
genome
music
bmr
calc-covg
updated 4 days ago by
Ram
37k • written 7.7 years ago by
qwertyuiop201320142015
• 0
1
vote
3
replies
264
views
Alphafold in Linux - HHblits error
linux
alphafold
3 days ago by
charlieclark1ee
▴ 10
1
vote
4
replies
156
views
trying to look the version of the programs under miniconda3 directory
miniconda3
versions
updated 2 days ago by
ATpoint
68k • written 2 days ago by
v.berriosfarias
▴ 90
1
vote
1
reply
201
views
Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver
set
webserver
enrichment
gene
analyses
updated 6 days ago by
ATpoint
68k • written 7 days ago by
fuellen
▴ 20
1
vote
1
reply
157
views
How to calculate tumor mutation burden (TMB)?
TMB
Mutations
WES
Sequencing
Mutationrate
updated 13 hours ago by
Fabio Marroni
★ 2.9k • written 18 days ago by
tanbiswas6
▴ 10
1
vote
5
replies
178
views
more than one sample in the same fasta file
mirnaseq
usegalaxy
3 days ago by
demoraesdiogo2017
▴ 80
1
vote
1
reply
447
views
Downloading the IMGT/V-QUEST software
vquest
software
updated 4 days ago by
H.Hasani
▴ 990 • written 14 months ago by
rubic
▴ 260
1
vote
1
reply
143
views
Plotting Correlation matrix
python
matrix
R
correlation
updated 1 day ago by
LChart
1.8k • written 1 day ago by
Zhiyi
• 0
1
vote
3
replies
175
views
Retrieve specific fasta sequences from a group of assemblies
CDS
gene
sequence
updated 1 day ago by
Matthias Zepper
2.8k • written 1 day ago by
SushiRoll
▴ 100
1
vote
1
reply
129
views
Variant annotation in fishes
Variant
Calling
annotation
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
Hayler Edu
▴ 30
1
vote
1
reply
137
views
Aggregate gene expression
AggregateExpression
RNASeq
Seurat
expression
gene
updated 1 day ago by
jv
▴ 740 • written 1 day ago by
Anst
▴ 30
1
vote
2
replies
225
views
Get all isoforms and proteins that correspond to list of Trinity gene IDs
fasta
grep
python
isoforms
5 days ago by
cdsparks
• 0
1
vote
1
reply
123
views
How to set NCBI entrez to pipe or ignore errors?
NCBI
Entrez
updated 1 day ago by
GenoMax
125k • written 1 day ago by
rijan_dhakal
• 0
1
vote
0
replies
107
views
cBioportal: Mutations in the database don't appear in the portal
cbioportal
1 day ago by
Camilo Andres
▴ 20
1
vote
1
reply
137
views
min.cells in CreateSeuratObject
Seurat
updated 5 days ago by
rpolicastro
10k • written 5 days ago by
jomo018
▴ 680
0
votes
0
replies
67
views
Display fraction of mutations and variants for Amplicon Sequencing sample?
PCR
Amplicon
VCF
BWA
3 days ago by
Saran
▴ 10
0
votes
0
replies
124
views
Differential Peak Analysis for a specific gene using only bigWig + BED files?
differential
peak
bigwig
chip-seq
analysis
1 day ago by
Maycon
• 0
0
votes
0
replies
86
views
STACKS pipeline. Confused about paired-end with "ustacks".
STACKS
2 days ago by
Roland
▴ 10
0
votes
1
reply
163
views
expansions and contractions from OrthoFinder
protein
python
orthofinder
updated 1 day ago by
mohammadhassanj
▴ 230 • written 2 days ago by
Ric
▴ 430
0
votes
0
replies
128
views
Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry
cellranger
5prime
PE
R2
V2
1 day ago by
ashley.fletcher2
• 0
0
votes
0
replies
111
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling
eukaryotic
transcriptomics
call
gene
4 days ago by
O.rka
▴ 640
0
votes
1
reply
166
views
Statistical test for checking cis regulation?
Genomics
Biostats
updated 18 hours ago by
Fabio Marroni
★ 2.9k • written 5 days ago by
lumos
• 0
0
votes
0
replies
2
views
a problem with getBM
and
getBM
biomart
just now by
sanaz
• 0
0
votes
0
replies
108
views
PennCNV - hg19 immunoglobulin region and crm region
spurrious
region
PennCNV
5 days ago by
Viktor Messi
• 0
0
votes
1
reply
1.2k
views
find NON Coding SNPs using annovar or ucsc genome browser
ucsc
SNP
orf
non-coding
annovar
updated 5 days ago by
Ram
37k • written 7.7 years ago by
pinikoma
• 0
138 results • Page
1 of 3
Recent Votes
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Recent Locations •
All
Israel,
6 minutes ago
Romania,
11 minutes ago
United States,
19 minutes ago
Bologna,
27 minutes ago
Manipal School of Life Science,
29 minutes ago
Malaysia,
32 minutes ago
Hong Kong,
34 minutes ago
Recent Awards •
All
Popular Question
to
tianshenbio
▴ 160
Popular Question
to
maxdlf12
• 0
Teacher
to
Pierre Lindenbaum
152k
Popular Question
to
LDT
▴ 220
Popular Question
to
Michael Dondrup
52k
Popular Question
to
caochch
• 0
Popular Question
to
timothy.kirkwood
▴ 130
Recent Replies
Answer: trainGlimmerHMM Error while training a genome
by
congliu37
• 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File?
by
Jeremy Leipzig
21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)?
by
Fabio Marroni
★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism
by
Rob
▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers
by
Pierre Lindenbaum
152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence
by
vvasta
• 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb?
by
Pierre Lindenbaum
152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation?
by
Fabio Marroni
★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2
by
Fabio Marroni
★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file**
by
Pierre Lindenbaum
152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4
by
Pierre Lindenbaum
152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
Comment: Error: unable to open file or unable to determine types for file bed file
by
Neel
▴ 10
**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
Answer: Anti-miRNA oligonuclotide identification
by
Asan Emirsale
• 0
You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file
by
vaslanzadeh
▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
Traffic: 813 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