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
4 of 20
Sort: Views
Rank
Views
Votes
Replies
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.9 years ago by
zorn21g
• 0
2
votes
1
reply
2.5k
views
Converting blastn output to VCF (for SNPs): what is the quickest way?
VCF
blast
SNP
xml
updated 10 months ago by
Ram
43k • written 6.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.5k
views
problem with updating trinity
software-error
trinity
updated 10 months ago by
Ram
43k • written 5.5 years ago by
ashokkumar.mb
• 0
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 16 months ago by
TN
• 0
4
votes
6
replies
2.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 11 months ago by
minakshiboruahassam
• 0 • written 21 months ago by
Plus
▴ 20
0
votes
0
replies
2.5k
views
Analysis and tools for gene/pathway conservation
evolution
updated 11 months ago by
Ram
43k • written 9.1 years ago by
hbw
▴ 90
0
votes
2
replies
2.5k
views
Error while running MEGAX
multiple-sequence-alignment
MEGAX
updated 12 months ago by
Ram
43k • written 6.0 years ago by
Mohak
▴ 20
2
votes
6
replies
2.5k
views
Basecalling with dorado
variants
dorado
alignment
methylation
nanopore
4 months ago by
eebloom
▴ 80
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence
python
updated 6 months ago by
Feng Tian
▴ 20 • written 5.6 years ago by
gewa
▴ 20
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 28 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
6
replies
2.4k
views
No best K value found
Assembly
Kmergenie
updated 5 months ago by
shaileshdesai76
• 0 • written 7.2 years ago by
kspata
▴ 80
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 7 weeks ago by
Ram
43k • written 6.2 years ago by
Sharon
▴ 610
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 12 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 27 days ago by
Ram
43k • written 4.9 years ago by
saksis.rihards
▴ 10
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV
WGS
updated 10 months ago by
Ram
43k • written 6.7 years ago by
zhang248
▴ 40
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 5 weeks ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
2
votes
20
replies
2.4k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
8 months ago by
Maxine
▴ 40
1
vote
2
replies
2.4k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 11 months ago by
barslmn
★ 2.1k • written 6.6 years ago by
shrutishreyajha
▴ 10
1
vote
3
replies
2.4k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 5 months ago by
ayaosama2111
▴ 10 • written 7.5 years ago by
Nicolas Rosewick
11k
1
vote
3
replies
2.4k
views
Use vcf files for dN/dS calculations
sequencing
updated 7 months ago by
rohitsatyam102
▴ 860 • written 6.4 years ago by
L. A. Liggett
▴ 120
0
votes
0
replies
2.4k
views
Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format
r
updated 11 months ago by
Ram
43k • written 10.6 years ago by
Jason
▴ 20
2
votes
5
replies
2.4k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 10 weeks ago by
xiaoleiusc
▴ 140 • written 5.9 years ago by
caggtaagtat
★ 1.9k
2
votes
2
replies
2.3k
views
bcftools annotate -a
bcftools
VCF
updated 10 months ago by
Ram
43k • written 14 months ago by
anasjamshed
▴ 120
1
vote
1
reply
2.3k
views
RStudio Cloud : Problem in Package Installing
RStudio
Bioconductor
updated 11 months ago by
Ram
43k • written 4.0 years ago by
Rishabh Jha
• 0
1
vote
0
replies
2.3k
views
Inflated qq plot and genomic inflation est. lambda
gene
SNP
genome
updated 10 months ago by
Ram
43k • written 6.0 years ago by
khn
▴ 130
0
votes
0
replies
2.3k
views
Slimming or not slimming with Gene Ontology: which tool should be used?
gene-ontology
go-annotation
updated 10 months ago by
Ram
43k • written 7.8 years ago by
tlorin
▴ 360
0
votes
1
reply
2.3k
views
Cochran-Armitage trend test
plink
updated 10 months ago by
Ram
43k • written 7.8 years ago by
toyan.j.p
▴ 30
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 210 • written 7 months ago by
Chris
▴ 280
1
vote
1
reply
2.3k
views
Tools for just generating a file including all shared variants in all VCF files
vcf
shared-variants
updated 11 months ago by
Ram
43k • written 7.8 years ago by
zengtony743
▴ 80
0
votes
11
replies
2.3k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 10 months ago by
Ram
43k • written 5.0 years ago by
saumya.sharma1509
• 0
2
votes
5
replies
2.3k
views
Reciprocal blast commandline
Blast
updated 10 months ago by
Ram
43k • written 4.8 years ago by
baurumon
▴ 30
1
vote
1
reply
2.3k
views
NS, AC, AN and AF in VCF file
VCF
updated 8 months ago by
Mwangana
• 0 • written 22 months ago by
wangdp123
▴ 340
0
votes
2
replies
2.3k
views
ROSE Algorithm for Ranking Super Enhancers
ChIP-Seq
updated 12 weeks ago by
Ram
43k • written 3.9 years ago by
mropri
▴ 150
0
votes
4
replies
2.3k
views
HOMER load genomes not working
HOMER
rna
pombe
genome
updated 11 months ago by
Ram
43k • written 3.9 years ago by
c78483
• 0
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by
smisek
• 0 • written 3.5 years ago by
ian_chiquier
• 0
1
vote
2
replies
2.2k
views
Quantitative anlysis of alternative splicing events
RNA-Seq
updated 10 months ago by
Ram
43k • written 9.7 years ago by
Anil Kesarwani
▴ 90
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral
genome
updated 9 weeks ago by
illodukarthickbabu
• 0 • written 2.7 years ago by
alslonik
▴ 310
0
votes
1
reply
2.2k
views
MACS2 result analysis
peak-calling
macs2
ChIP-Seq
updated 10 months ago by
Ram
43k • written 5.0 years ago by
chaudharyc61
▴ 90
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 27 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein
transcript
normalisation
updated 3 months ago by
Ram
43k • written 21 months ago by
qiz218591
▴ 10
0
votes
5
replies
2.2k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 11 months ago by
Ram
43k • written 7.8 years ago by
yoyofangliu
• 0
0
votes
1
reply
2.2k
views
monocle how to identify branches
RNA-Seq
pseudotime
monocle
updated 10 months ago by
Ram
43k • written 5.6 years ago by
hsu
▴ 40
0
votes
3
replies
2.2k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 7 months ago by
aishwarya
• 0 • written 5.9 years ago by
blooming.daisy333
▴ 110
0
votes
3
replies
2.2k
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
11 months ago by
Mo
▴ 40
0
votes
1
reply
2.2k
views
hmmsearch didn't work with nucleotide genome
genome
hmmsearch
HMMER
updated 10 months ago by
Ram
43k • written 6.2 years ago by
lbroetto
• 0
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end
alignment
next-gen
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Kenneth Daily
▴ 50
2
votes
13
replies
2.2k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 7 months ago by
Ram
43k • written 9 months ago by
epianalysis
• 0
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by
Ram
43k • written 9.1 years ago by
Harish Sanja
▴ 10
0
votes
5
replies
2.1k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax
genomics
Cpp
plink
GWAS
updated 10 months ago by
linchenshitiancai
• 0 • written 6.2 years ago by
michael.nagle
▴ 100
0
votes
2
replies
2.1k
views
Tool for manual annotation curation
annotation
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Rox
★ 1.4k
1,000 results • Page
4 of 20
Recent Votes
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Recent Locations •
All
Bangladesh,
3 minutes ago
United States,
8 minutes ago
Singapore,
12 minutes ago
Portugal,
15 minutes ago
Canada,
16 minutes ago
Australia,
18 minutes ago
Japan,
19 minutes ago
Recent Awards •
All
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Popular Question
to
jen
▴ 10
Popular Question
to
nitinra
▴ 50
Scholar
to
Pierre Lindenbaum
161k
Scholar
to
Ram
43k
Popular Question
to
bioinfo
▴ 150
Recent Replies
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Traffic: 2106 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