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 year
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Votes
Rank
Views
Votes
Replies
23
votes
22
replies
43k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 9 months ago by
Nicole
• 0 • written 5.4 years ago by
gaelgarcia
▴ 250
22
votes
20
replies
2.2k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 5 months ago by
Ram
40k • written 7.2 years ago by
Farbod
★ 3.4k
20
votes
17
replies
2.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 11 weeks ago by
1769mkc
★ 1.1k • written 2.6 years ago by
pomodoro_sinensis
▴ 110
18
votes
19
replies
1.9k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 9 months ago by
Ram
40k • written 4.7 years ago by
rbkh09
• 0
18
votes
4
replies
8.3k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 6 months ago by
Ram
40k • written 10.1 years ago by
user
▴ 940
14
votes
5
replies
2.9k
views
bioinformatics basic training
genome
updated 6 months ago by
Ram
40k • written 8.8 years ago by
f.muoghalu
• 0
12
votes
13
replies
2.4k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 9 months ago by
Ram
40k • written 8.2 years ago by
sarathkurichiyil
• 0
11
votes
9
replies
2.3k
views
samtools piping with awk/ bash commands -> Wonky things happen!!!
bash
samtools
awk
updated 9 months ago by
Ram
40k • written 8.3 years ago by
QVINTVS_FABIVS_MAXIMVS
★ 2.5k
10
votes
7
replies
3.4k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 3 months ago by
Ram
40k • written 7.4 years ago by
Pranavathiyani G
▴ 330
10
votes
14
replies
4.3k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 3 months ago by
Ram
40k • written 3.6 years ago by
gable_works
▴ 50
10
votes
6
replies
689
views
RNA seq, secreted protein
protein
gene
secreted
updated 7 weeks ago by
Joe
21k • written 9 months ago by
Rob
▴ 160
10
votes
6
replies
2.7k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 6 months ago by
Ram
40k • written 8.3 years ago by
lait
▴ 180
10
votes
15
replies
5.6k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 6 months ago by
Ram
40k • written 5.0 years ago by
marongiu.luigi
▴ 690
10
votes
15
replies
1.3k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
3 months ago by
Chris
▴ 180
9
votes
20
replies
3.6k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 6 months ago by
Ram
40k • written 5.1 years ago by
marongiu.luigi
▴ 690
9
votes
16
replies
3.3k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 6 months ago by
Ram
40k • written 5.1 years ago by
marongiu.luigi
▴ 690
9
votes
7
replies
989
views
Reference genome location
reference
positions
FASTA
alignment
genome
updated 8 months ago by
barslmn
★ 1.8k • written 8 months ago by
Batel
• 0
9
votes
5
replies
419
views
Prophage prediction tool
prophage
PHASTER
prediction
updated 9 weeks ago by
GenoMax
134k • written 9 weeks ago by
A_heath
▴ 140
9
votes
4
replies
1.6k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 5 months ago by
Ram
40k • written 7.1 years ago by
Bilal
▴ 60
9
votes
4
replies
5.3k
views
How to analyse normalized read count?
RNA-Seq
R
updated 8 months ago by
Ram
40k • written 8.3 years ago by
pbio
▴ 150
9
votes
13
replies
13k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 3 months ago by
Ram
40k • written 5.0 years ago by
Shahzad
▴ 30
8
votes
13
replies
1.2k
views
Mapped reads not mapping to a real sequence?
bam
sam
samtools
kallisto
7 months ago by
txema.heredia
▴ 80
8
votes
10
replies
1.4k
views
PyWGCNA
WGCNA
3 months ago by
yoshifumimiya
▴ 40
8
votes
9
replies
2.8k
views
error in rstudio
csv
matrix
rstudio
updated 12 months ago by
Ram
40k • written 8.1 years ago by
fi1d18
★ 4.2k
8
votes
4
replies
1.8k
views
using different tools to identify differential exprssed genes
rna-seq
RNA-Seq
R
updated 12 months ago by
Ram
40k • written 8.1 years ago by
Anushka
▴ 20
8
votes
5
replies
1.6k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 3 days ago by
Ram
40k • written 23 months ago by
A_heath
▴ 140
8
votes
3
replies
840
views
Package installation error using Bioconda
antismash
Bioconda
9 months ago by
A_heath
▴ 140
8
votes
25
replies
2.4k
views
construction of a database
sql
noSQL
neo4j
database
updated 6 months ago by
Ram
40k • written 2.3 years ago by
Debut
▴ 20
8
votes
6
replies
994
views
How to apply bioinformatic in vaccine design?
Vaccine
updated 10 months ago by
Dunois
★ 2.4k • written 10 months ago by
Jean
▴ 50
8
votes
5
replies
3.3k
views
Is it possible to guess sequencing platform used based on a FASTQ/BAM file?
BAM
FASTQ
updated 9 months ago by
Ram
40k • written 8.3 years ago by
Andrew
▴ 60
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 10 months ago by
Ram
40k • written 8.2 years ago by
biolab
★ 1.4k
8
votes
7
replies
728
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf
VEP
3 months ago by
Jeremy Leipzig
21k
8
votes
12
replies
3.1k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 6 months ago by
Ram
40k • written 2.1 years ago by
daver.v
▴ 30
7
votes
7
replies
4.6k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 3 months ago by
Ram
40k • written 4.7 years ago by
stu111538
▴ 80
7
votes
10
replies
1.4k
views
col as names [solved]
R
updated 6 months ago by
Ram
40k • written 4.5 years ago by
demoraesdiogo2017
▴ 90
7
votes
4
replies
1.4k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 6 months ago by
Ram
40k • written 5.2 years ago by
healing80
• 0
7
votes
2
replies
3.2k
views
Counting reads for gene transcripts with overlapping loci
RNA-Seq
gene
R
updated 8 months ago by
Ram
40k • written 8.3 years ago by
Ruet
▴ 70
7
votes
8
replies
2.6k
views
Discrepency between number of reads tophat
RNA-Seq
tophat
software-error
updated 12 months ago by
Ram
40k • written 8.1 years ago by
mbio.kyle
▴ 380
7
votes
8
replies
8.6k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 4 weeks ago by
Ram
40k • written 7.4 years ago by
nikelle.petrillo
▴ 110
7
votes
12
replies
1.1k
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 4 months ago by
Sasha
▴ 720 • written 4 months ago by
Chris
▴ 180
7
votes
6
replies
1.7k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 6 months ago by
Ram
40k • written 22 months ago by
Nikhil
▴ 10
7
votes
8
replies
1.8k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 7 months ago by
Ram
40k • written 8.4 years ago by
xiaofeng.dong12
▴ 20
7
votes
4
replies
1.4k
views
microarray gene datasets
gene
updated 7 months ago by
Ram
40k • written 8.4 years ago by
bioinfo
▴ 60
7
votes
6
replies
840
views
On "wings" in volcano plots...
DEG
volcano
DGE
statistics
DE
updated 4 months ago by
ATpoint
76k • written 4 months ago by
kalavattam
▴ 180
7
votes
10
replies
1.5k
views
Ubuntu 20.04 Crash
Ubuntu
updated 7 months ago by
Ram
40k • written 20 months ago by
bala
• 0
7
votes
5
replies
2.3k
views
using machine learning regards to ribo-seq data sets
gene-regulatory-network
ribo-seq
machine-learning
updated 11 months ago by
Ram
40k • written 8.1 years ago by
fi1d18
★ 4.2k
7
votes
7
replies
1.6k
views
Sort and convert the SAM files to BAM
samtools
RNA-seq
NGS
updated 4 weeks ago by
Ram
40k • written 5.2 years ago by
amitunited0532
▴ 40
7
votes
4
replies
1.8k
views
useful and freely available softwares for Bioinformatics
software
updated 6 months ago by
Ram
40k • written 8.5 years ago by
Mo
▴ 920
7
votes
4
replies
4.1k
views
IGV genome browser problems
igv
updated 9 months ago by
Ram
40k • written 8.2 years ago by
Marvin
▴ 210
7
votes
8
replies
3.6k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 3 months ago by
Ram
40k • written 3.3 years ago by
kand3e
▴ 60
1,000 results • Page
1 of 20
Recent Votes
Comment: How to create structural variants ground truth for alignment of two long-read ge
Comment: Low Alignment rate
Answer: How to retrieve LoF and missense variants in WES data?
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
Comment: Hisat2 index and alignment question
Recent Locations •
All
India,
just now
United States,
1 minute ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
2 minutes ago
India,
3 minutes ago
Germany,
4 minutes ago
United Kingdom,
5 minutes ago
Argentina,
5 minutes ago
Recent Awards •
All
Popular Question
to
amy__
▴ 150
Popular Question
to
David Langenberger
10k
Popular Question
to
pablo
▴ 280
Scholar
to
Pierre Lindenbaum
157k
Popular Question
to
octpus616
▴ 80
Commentator
to
dsull
★ 4.7k
Popular Question
to
rbronste
▴ 420
Recent Replies
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
ATpoint
76k
Generally these genes are highly expressed, so there would be some sort of a power bias. How do you do the DE analysis? Any cutoffs on mini…
Answer: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2
by
David Langenberger
10k
:: LAST CALL :: Apply now, if you want to join this online workshop!
Answer: how to identify uniq genes between two gff files.
by
Juke34
8.2k
You can run `agat_sp_compare_two_annotations.pl` from [AGAT][1], you should get the information you are looking for. This method allow to c…
Comment: How to find out what adapters to remove after FastQC of RNAseq data?
by
ella
• 0
Thank you for the fast help, I have the BBMap suite installed anyways and will try it out :)
Comment: How to make alpha diversity boxplot?
by
yeah
• 0
thanks a lot! can't believe that is so simple
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes got it, thank you very much.
Comment: SCENIC-openloom not working
by
kyriakds
• 0
Hello, Did you find a solution in the end?
Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
Vijith
▴ 30
@swbarnes2, thanks for the response, by the way, can you tell me why/ how this happens during the sequencing process, and if it could negat…
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
> can you explain this ?? yes. you should use options like `-u` . > Write original A entry once if any overlaps found in B. In other word…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
Pierre Lindenbaum
157k
so validate the answer to close the question please (Green tick on the left).
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
hi Pierre Linderbaum, after extracting genes, I have 5846 genes in afile.bed and 4456 genes in bfile.bed , while using bedtools intersec…
Comment: how to extract unique snps in a vcf file by comparing with multiple vcf files
by
nikhil
▴ 10
thank you, bcftools isec is working well.
Comment: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
please, comment or validate the answers to your previous questions: https://www.biostars.org/p/9573151/#9573158 ; https://www.biostars.org/…
Answer: how to identify uniq genes between two gff files.
by
Pierre Lindenbaum
157k
extract genes (e.g: awk '($3=="gene") {printf("%s\t%d\t%s\n",$1;int($4)-1,$5);}' ) from both files n sort, and use bedtools intersect with…
Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
G is the letter you get if there is no fluorescence. 75% of your reads have a lot of G. I don't think this run worked.
Traffic: 1834 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