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 month
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
184
views
Trimmomatic
Sequence
change
distribution
after
length
updated 1 day ago by
Meisam
• 0 • written 1 day ago by
wonde2000
• 0
0
votes
1
reply
155
views
small RNA sequencing
smallRNA
Sequencing
updated 1 day ago by
Buffo
★ 2.0k • written 1 day ago by
mbansal
• 0
0
votes
1
reply
125
views
Transverse data
EXCEL
Unix
updated 1 day ago by
Pierre Lindenbaum
152k • written 1 day ago by
Sidra
• 0
0
votes
0
replies
93
views
GDCPrepare error (No such process)
TCGABiolinks
GDCPrepare
1 day ago by
aUser
▴ 20
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
1
vote
3
replies
225
views
"Error parsing strand (?) from GFF line" happenning in gffread, stringtie and cufflinks
bioinformatics
gffread
gff
stringtie
cufflinks
updated 1 day ago by
Pierre Lindenbaum
152k • written 2 days ago by
Guilherme
• 0
1
vote
1
reply
157
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq
long-reads
normalization
short-reads
updated 2 days ago by
Shiyi
▴ 20 • written 2 days ago by
Bernardo
• 0
2
votes
3
replies
468
views
setting up Kallisto software
rnaseqanalysis
anaconda
kalliosto
miniconda
software
updated 2 days ago by
ATpoint
68k • written 6 months ago by
bioinformatics
▴ 10
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
0
votes
6
replies
646
views
Best tools for scTCR-seq (VDJ) analysis?
scTCR-seq
updated 2 days ago by
Ming Tang
★ 2.9k • written 9 months ago by
yueli7
▴ 240
0
votes
0
replies
94
views
ORFik: error making Txdb from GTF and fasta files
gff3
gtf
ORFik
2 days ago by
Estefania
▴ 10
0
votes
1
reply
114
views
SetAllIdents and Idents function not found
scrna-seq
updated 2 days ago by
Mensur Dlakic
★ 22k • written 2 days ago by
bioinformatics.girl
• 0
0
votes
0
replies
100
views
bwa: reads aligned concordantly exactly 1 time
bowtie2
samtools
hisat2
alignment
bwa
2 days ago by
poecile.pal
▴ 40
0
votes
1
reply
275
views
Questions on analyzing TCGA proteome profiling data.
proteome
R
TCGA
updated 2 days ago by
pilargmarch
▴ 10 • written 14 days ago by
walden
• 0
0
votes
2
replies
241
views
differential gene expression pipelines rnaflow vs rnaseq
differential
expression
gene
1 day ago by
Agamemnon
▴ 60
8
votes
6
replies
323
views
Gene Set Enrichment Analysis, pathway, metabolism
metabolism
pathway
GSEA
9 hours ago by
Rob
▴ 160
4
votes
6
replies
296
views
What does it mean in GSEA when HALLMARK_UV_RESPONSE_DN is upregulated ? how it's down and upregulated?
GSEA
HALLMARK
2 days ago by
Amr
▴ 140
2
votes
2
replies
171
views
Do I need to correct for sequencing depth in bulk RNA seq?
seq
kallisto
rna
updated 2 days ago by
Ming Tang
★ 2.9k • written 2 days ago by
bioinfo
▴ 20
1
vote
1
reply
147
views
isoform compostion (psi) question
composition
isoform
updated 2 days ago by
i.sudbery
16k • written 3 days ago by
Jjbox
▴ 30
3
votes
2
replies
148
views
Peak Calling on a single gene?
chip
peak
illumina
calling
chip-seq
updated 2 days ago by
ATpoint
68k • written 2 days ago by
Maycon
• 0
0
votes
1
reply
108
views
Extracting region from alternate genome
fasta
extract
alternatereference
gatk
updated 2 days ago by
GenoMax
125k • written 2 days ago by
Ana
• 0
39
votes
11
replies
15k
views
11 follow
Best Database Of Transcription Factor Binding Sites
transcription
binding
database
updated 2 days ago by
nta
• 0 • written 11.9 years ago by
Dataminer
★ 2.7k
0
votes
1
reply
105
views
cluster profiler for pathway analysis in scRNA Seq
cluster
cell
Seurat
sequencing
Studio
profiler
Single
R
updated 2 days ago by
MRemod
• 0 • written 2 days ago by
mfro
• 0
2
votes
2
replies
4.0k
views
Advantages of Biobase's TRANSFAC over and above what is freely available?
TRANSFAC
Transcription
Regulation
UCSC
TFBS
updated 2 days ago by
nta
• 0 • written 8.7 years ago by
vlaufer
▴ 280
1
vote
4
replies
153
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
24
votes
10
replies
6.8k
views
7 follow
Is Transfac Professional Worth The Price?
updated 2 days ago by
nta
• 0 • written 9.8 years ago by
Tky
★ 1.0k
2
votes
3
replies
239
views
Problem with NextDenovo fungal assembly
Assembly
NextDenovo
Genome
updated 2 days ago by
colindaven
4.4k • written 6 days ago by
naveedkhanchemist
• 0
4
votes
5
replies
201
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
0
votes
1
reply
145
views
PHG Load haplotype and create consensus
haplotype
Consensus
PHG
updated 2 days ago by
lcj34
▴ 110 • written 2 days ago by
지용
• 0
2
votes
4
replies
173
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
0
votes
0
replies
86
views
STACKS pipeline. Confused about paired-end with "ustacks".
STACKS
2 days ago by
Roland
▴ 10
2
votes
7
replies
1.3k
views
Normalizing TCR data
Analysis
updated 2 days ago by
Ming Tang
★ 2.9k • written 3.9 years ago by
ruchitkpanchal
• 0
0
votes
1
reply
128
views
Which RUVr batch corrected output is better to calculate TPM?
RUVSeq
RNA-seq
batch_effect
TPM
R
updated 2 days ago by
ATpoint
68k • written 2 days ago by
star
▴ 330
0
votes
4
replies
236
views
Running command in docker container results in directly shutting down the docker container
docker-container
python
ubuntu
docker
1 day ago by
stan.aanhane
▴ 30
0
votes
1
reply
127
views
MetaWRAP databases on external HDD
metagenomics
metaWRAP
KRAKEN
updated 2 days ago by
GenoMax
125k • written 2 days ago by
Raz
• 0
0
votes
2
replies
198
views
Bioconductor drawProteins alternative in Python
protein
python
schematics
1 day ago by
D3xt3R
• 0
2
votes
6
replies
1.2k
views
Can we get absolute abundance of TCR using TCR-Seq?
TCR-Seq
updated 2 days ago by
mizraelson
▴ 40 • written 4.1 years ago by
CY
▴ 710
1
vote
4
replies
1.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR
shannon
simpson
updated 2 days ago by
mizraelson
▴ 40 • written 3.8 years ago by
CY
▴ 710
1
vote
3
replies
237
views
How can I construct the adjacency matrix for gene ontology between genes
GeneOntology
python
GO
updated 2 days ago by
barslmn
★ 1.2k • written 2 days ago by
songyeon0425
• 0
0
votes
1
reply
143
views
Tag SNPs
HLA
SNPs
Sequence
Tag
updated 1 day ago by
Fabio Marroni
★ 2.9k • written 2 days ago by
Koustav Maiti
• 0
5
votes
6
replies
293
views
Mapping a small number of contigs to a reference subsequence
align
genome
mapping
assembly
contigs
updated 2 days ago by
cmdcolin
★ 2.7k • written 3 days ago by
alexandru.bologa.marian
▴ 30
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
1
reply
235
views
How to find UMI counts from cell ranger VDJ output
cellranger
updated 3 days ago by
mizraelson
▴ 40 • written 10 weeks ago by
Kevin
▴ 50
4
votes
4
replies
579
views
How to do typing of VDJ regions for10x TCR kit?
TCRA
Immunology
TCR
updated 3 days ago by
mizraelson
▴ 40 • written 5 months ago by
MohammadAlkadi
▴ 70
6
votes
5
replies
4.3k
views
6 follow
Length Of The Vdj Segment In B Cells
recombination
updated 3 days ago by
mizraelson
▴ 40 • written 9.6 years ago by
ericmajinglong
▴ 120
1
vote
4
replies
393
views
filter out T cell clones
vdjtools
TCR
mixcr
bulk
updated 2 days ago by
Jesse
▴ 450 • written 10 weeks ago by
chi.delta
▴ 40
5
votes
4
replies
581
views
Help and idea with TCR/BCR analysis
BCR
TCR
scRNA-seq
updated 3 days ago by
mizraelson
▴ 40 • written 3 months ago by
fi1d18
★ 4.1k
0
votes
4
replies
822
views
Detection T cell receptor transcripts
RNA-Seq
sequence
next-gen
updated 3 days ago by
mizraelson
▴ 40 • written 2.5 years ago by
jsw940
▴ 10
0
votes
1
reply
556
views
Comparing 5'RACE TCR Sequencing Methods
TCR
5'RACE
repertoire
MiXCR
clones
updated 3 days ago by
mizraelson
▴ 40 • written 2.6 years ago by
tdfyoder
▴ 40
0
votes
2
replies
1.8k
views
TCR data analysis
next-gen
TCR
updated 3 days ago by
mizraelson
▴ 40 • written 3.9 years ago by
bthomas4
• 0
1,000 results • Page
2 of 20
Recent Votes
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
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Recent Locations •
All
United States,
4 minutes ago
Hong Kong,
14 minutes ago
Natal, Brazil,
15 minutes ago
United States,
35 minutes ago
Brazil,
38 minutes ago
United States,
45 minutes ago
USA,
48 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: 844 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