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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
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
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 21 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
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
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
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
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
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
2
votes
6
replies
2.5k
views
Basecalling with dorado
variants
dorado
alignment
methylation
nanopore
4 months ago by
eebloom
▴ 80
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 27 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
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
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
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 26 days ago by
Ram
43k • written 4.9 years ago by
saksis.rihards
▴ 10
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 11 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
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 6 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
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
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
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
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
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
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
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
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
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
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
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
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 26 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
3
votes
7
replies
2.2k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance
RNA-SEQ
RSEM
Trinity
updated 12 months ago by
Ram
43k • written 2.6 years ago by
Princy
▴ 60
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
1,000 results • Page
4 of 20
Recent Votes
Error: htsjdk.tribble.TribbleExpection: The provided VCF file is malformed at approximately line number 5880: Duplicate allele added to VariantContext: GT
Answer: Process Truncated fastq file
The Biostar Herald for Monday, May 13, 2024
C: What % of rRNA contamination is acceptable?
A: What % of rRNA contamination is acceptable?
A: GC bias correction for Chip-SEQ
Comment: Help with IGV abbreviation
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Recent Replies
Comment: RNAseq RNA content
by
ATpoint
82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object
by
ATpoint
82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
by
J.
▴ 10
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs?
by
GenoMax
142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs?
by
i.sudbery
19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq
by
ATpoint
82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
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by
i.sudbery
19k
Which species is this?
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
by
ATpoint
82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error
by
trkfs
• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
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