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717 results • Page
2 of 15
Sort: Votes
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Votes
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7
votes
13
replies
3.3k
views
8 follow
Doubt - installing LncTar software
software installation
Lnctar
perl
updated 6 days ago by
Jeremiah
• 0 • written 3.8 years ago by
kousi31
▴ 50
7
votes
6
replies
1.4k
views
Forum:
Bioinformaticians - Am I on the Right Track?
Career
updated 19 hours ago by
Ram
39k • written 3.5 years ago by
kstangline
▴ 70
7
votes
6
replies
306
views
Contigs to chromosomes annotation
Assembly
mapping
contigs
updated 17 hours ago by
GenoMax
129k • written 1 day ago by
alexandru.bologa.marian
▴ 50
7
votes
6
replies
1.1k
views
Job:
Come work with me! Bioinformatician - Boston MA
job
updated 2 days ago by
Joseph
• 0 • written 8 months ago by
Devon Ryan
103k
7
votes
17
replies
7.3k
views
10 follow
Python FASTA scripting
Python
FASTA
updated 1 day ago by
Ram
39k • written 3.7 years ago by
damonlbp
▴ 20
6
votes
5
replies
5.3k
views
BWA aln - failed to locate the index
alignment
bwa
updated 4 days ago by
Ram
39k • written 3.7 years ago by
m.wekking
▴ 10
6
votes
8
replies
616
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
5 hours ago by
Chris
▴ 100
6
votes
6
replies
1.1k
views
Want read count with respect to geneID instead of transcript IDs
RNA-Seq
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
archana.bioinfo87
▴ 180
6
votes
5
replies
713
views
Forum:
Tips on: How to organise data on servers
genotype
warehouse
servers
updated 20 hours ago by
Ram
39k • written 3.5 years ago by
flight505
▴ 90
6
votes
7
replies
350
views
NCBI API, Perl
API
NCBI
updated 1 day ago by
GenoMax
129k • written 1 day ago by
alessandro.alma00
• 0
6
votes
7
replies
3.6k
views
7 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq
diffbind
updated 1 day ago by
Jo
• 0 • written 3.7 years ago by
m.sadman.sakib
▴ 120
6
votes
0
replies
808
views
News:
CWL user support moving to https://cwl.discourse.group/; many thanks to Biostars for over 4 years of support!
cwl
thanks
updated 1 day ago by
Ram
39k • written 3.6 years ago by
Michael R. Crusoe
★ 1.9k
6
votes
5
replies
1.1k
views
7 follow
Forum:
What do you think of sci-hub?
sci-hub
updated 18 hours ago by
Ram
39k • written 3.4 years ago by
cduukj
• 0
6
votes
17
replies
4.5k
views
8 follow
Eigen genes using WGCNA
wgcna
eigengenes
updated 1 day ago by
chaco001
▴ 40 • written 4.7 years ago by
shivangi.agarwal800
▴ 120
5
votes
3
replies
1.1k
views
Introduction to Structural Bioinformatics
protein
structural-bioinformatics
updated 6 days ago by
Ram
39k • written 4.0 years ago by
iamakhilverma
• 0
5
votes
4
replies
777
views
IQ-TREE stuck in selecting a substitution model with ModelFinder
substitution
ModelFInder
model
IQ-TREE
updated 4 hours ago by
rohitsatyam102
▴ 690 • written 10 months ago by
Begonia_pavonina
▴ 100
5
votes
2
replies
731
views
News:
The precisionFDA BioCompute Object App-a-thon has been extended to October 18!
BioCompute
challenge
updated 5 days ago by
Ram
39k • written 3.9 years ago by
hollystephens723
▴ 70
5
votes
3
replies
712
views
Forum:
price of MSI detection by NGS for 1 person
next-gen
updated 6 days ago by
Ram
39k • written 3.9 years ago by
jandoubi.nouha333
▴ 20
5
votes
0
replies
999
views
Job:
Postdoctoral Scientist (Bioinformatics) at The Earlham Institute, UK
genome
methylation
sequencing
updated 5 days ago by
Ram
39k • written 3.9 years ago by
El Blanco
▴ 40
5
votes
6
replies
449
views
Inquiry Regarding Somatic Analysis and Normal Sample Requirement
ngs
somatic
germline
updated 6 days ago by
Ram
39k • written 14 days ago by
Nour-eddine
▴ 30
5
votes
6
replies
423
views
How to calculate TPM from featureCounts output
rna-seq
TPM
featurecounts
5 hours ago by
survive
• 0
5
votes
5
replies
2.0k
views
Forum:
BCL files as deliverables from a sequencing center
core-facility
service-provider
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Ido Tamir
5.2k
5
votes
2
replies
213
views
How to detect specific genes in metagenomics data
metagenomics
genes
updated 5 days ago by
Ram
39k • written 5 days ago by
aziznasr1920
▴ 10
5
votes
7
replies
1.7k
views
How to prevent reduce from being performed in GRanges during setdiff
blunt-end
genomicranges
setdiff
updated 5 days ago by
hossiny
• 0 • written 2.3 years ago by
Bosberg
▴ 50
5
votes
3
replies
4.0k
views
What Do Chromosome Codes Such As 'Chr_Random' Represent?
plink
chromosome
updated 6 days ago by
Ram
39k • written 10.8 years ago by
zhuwei.cug
▴ 30
5
votes
5
replies
1.4k
views
Improve illumina short read assembly using PacBio long reads
Assembly
Illumina
genome
PacBio
updated 6 days ago by
Ram
39k • written 4.1 years ago by
shachigahoimbi
▴ 20
4
votes
4
replies
888
views
Forum:
Kubernetes in Production?
ci-cd
webservice
kubernetes
docker
updated 17 hours ago by
Ram
39k • written 3.5 years ago by
acamukhin
• 0
4
votes
4
replies
1.4k
views
Forum:
When will the hg19/grch37 finally become obsolete?
Reference-Genome
updated 6 days ago by
Ram
39k • written 4.0 years ago by
gdaly9000
▴ 10
4
votes
3
replies
307
views
What does canonical transcript mean in the context of VEP
vep
updated 4 days ago by
Vincent Laufer
★ 2.9k • written 4 days ago by
curious
▴ 720
4
votes
11
replies
1.8k
views
6 follow
The fastest protein sequence aligner available
protein
sequence
alignment
updated 5 days ago by
Alexander
▴ 70 • written 5.0 years ago by
Bioaln
▴ 360
4
votes
4
replies
334
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
1 day ago by
sodiumnitrate
▴ 20
4
votes
1
reply
977
views
News:
Bioinformatics Workflows with Nextflow
Netflow
reproducibility
Workflows
updated 17 hours ago by
Ram
39k • written 3.5 years ago by
carlopecoraro2
★ 2.3k
4
votes
8
replies
769
views
VEP tab/vcf - Different output
VEP
ensembl
updated 22 hours ago by
Ben_Ensembl
★ 2.2k • written 14 months ago by
Filago
▴ 90
4
votes
4
replies
293
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 5 days ago by
bioinfo
▴ 80
4
votes
12
replies
840
views
Separating text from one column in R
R
updated 6 days ago by
Ram
39k • written 4.0 years ago by
e.jabbari
• 0
4
votes
6
replies
316
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 5 days ago by
Ram
39k • written 6 days ago by
abbas.waseem.gcu
▴ 20
4
votes
0
replies
768
views
Forum:
Help make UMI-tools even better - take our survey
Survey
UMI
UMI-Tools
updated 1 day ago by
Ram
39k • written 3.6 years ago by
i.sudbery
17k
4
votes
2
replies
1.1k
views
News:
Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop
methylation
bisulfite
updated 1 day ago by
Ram
39k • written 3.7 years ago by
Lars
▴ 970
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
4
votes
5
replies
594
views
how to design a guide RNA
genomics
updated 5 days ago by
rfran010
▴ 160 • written 18 days ago by
Bioinfo
• 0
4
votes
3
replies
609
views
Precision-recall curve to compare metagenome classifiers to a gold standard - Is this even a viable method?
classification
recall
precision
metagenome
updated 6 days ago by
sneha.d
• 0 • written 10 months ago by
Bertalan_Takacs
▴ 90
4
votes
7
replies
5.2k
views
Help making ADMIXTURE output digestible
admixture
updated 6 days ago by
Aaron
▴ 20 • written 7.8 years ago by
devenvyas
▴ 730
4
votes
4
replies
990
views
Forum:
What skills are required for an informatics scientist?
informatics
scientist
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Shicheng Guo
★ 9.3k
4
votes
0
replies
1.3k
views
Job:
Four 4-year PhD studentships @ the Van de Peer Lab (VIB-UGent, Ghent, Belgium)
PhD
evolution
genomics
updated 4 days ago by
Ram
39k • written 3.7 years ago by
lieven.sterck
14k
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
4
votes
5
replies
13k
views
Take A Subset Of A Fastq Paired-End Sample
paired-end
fastq
rna-seq
illumina
updated 6 days ago by
Ram
39k • written 10.2 years ago by
dfernan
▴ 730
4
votes
12
replies
1.2k
views
Forum:
publicly available data
arrayexpress
GEO
SRA
updated 1 day ago by
Ram
39k • written 3.7 years ago by
Konstantinos Yeles
▴ 110
4
votes
13
replies
1.3k
views
Forum:
Looking for Participants: Meenta NovaSeq RunShare Beta
RunShare
next-gen
NovaSeq
updated 5 days ago by
Ram
39k • written 3.9 years ago by
Torrey Ah-Tye
▴ 10
4
votes
0
replies
915
views
Forum:
Plotting Ensembl gene name changes between versions
R
ensembl
updated 4 days ago by
Ram
39k • written 3.8 years ago by
Corentin
▴ 550
4
votes
2
replies
178
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 5 days ago by
chrchang523
10k • written 6 days ago by
rj.rezwan
• 0
717 results • Page
2 of 15
Recent Votes
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
Answer: Alignment of case vs. control from different origin
Comment: Alignment of case vs. control from different origin
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Recent Replies
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing an intercept equal to zero instead of testing for a logFC. I wonder what comparison you were t…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. These are raw counts.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Ayish
• 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix?
by
Thu
• 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software
by
Darked89
4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin
by
sativus
▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs
by
colindaven
4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
> but none of them work for me https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried this one before but the output file is empty
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried all of them but none of them work for me
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