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121,054 results • Page
1 of 2422
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0
votes
0
replies
13
views
pLoF variants for gnomAD v.4
gnomAD
pLoF
variants
grch38
1 hour ago by
Damianos P. Melidis
▴ 40
1
vote
0
replies
146
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
3 hours ago by
Pierre Lindenbaum
166k
0
votes
1
reply
70
views
Genomic Data Portal (GDC) download a given a link file
GDC
R
TCGA
TCGAbiolinks
maftools
4 hours ago by
bioinformagician
• 0
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 14 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
4
replies
116
views
How to generate identiy score between aligned sequences with Mauve?
identity
score
alignment
mauve
3 hours ago by
marongiu.luigi
▴ 740
5
votes
7
replies
2.3k
views
6 follow
Cluster annotation in single cell
Single-cell
updated 19 hours ago by
Shiyang
• 0 • written 19 months ago by
synat.keam
▴ 100
0
votes
1
reply
148
views
Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under the same condition
rna-seq
ribo-seq
translation-efficiency
dataset-search
nicotiana-benthamiana
updated 21 hours ago by
colindaven
7.4k • written 1 day ago by
Farshid
• 0
0
votes
4
replies
398
views
Limma model gives weird results
model
multivariate
Limma
updated 1 day ago by
SamGG
▴ 90 • written 3 days ago by
leranwangcs
▴ 150
3
votes
4
replies
406
views
How to download the entire C. elegans genome from WormBase into Excel with automated gene descriptions
Gene
Wormbase
Celegans
updated 1 day ago by
GenoMax
151k • written 2 days ago by
bioinformatics_rk
▴ 10
0
votes
0
replies
124
views
Job:
Postdoctoral Research Fellow, multi-omics, Univ of Nebraska Medical Center, Omaha, NE, USA
microbiome
Postdoc
metagenome
transcriptome
metabolome
updated 1 day ago by
GenoMax
151k • written 1 day ago by
era
• 0
0
votes
0
replies
128
views
How to deal with the clusterProfiler analysis result?
clusterProfiler
updated 1 day ago by
GenoMax
151k • written 2 days ago by
Tundup
• 0
0
votes
0
replies
144
views
News:
Genome Bioinformatics Summer School: OMICSS-25
training
bioinformatics
school
2 days ago by
Lilit
• 0
1
vote
2
replies
218
views
Unable to find mitochondrial genes in latest rat genome(GRCr8)
seurat
genome
mitochondrialgenes
NCBI
Singlecell
2 days ago by
dxj294
• 0
0
votes
0
replies
113
views
Haplotype reference for ShapeIt (ShapeIt5)
Phasing
2 days ago by
evan.kransdorf
• 0
6
votes
6
replies
316
views
Pre-Made STAR Index for mm10 Mouse Genome
STAR
updated 22 hours ago by
colindaven
7.4k • written 2 days ago by
Nerelys
• 0
1
vote
1
reply
179
views
The volcano plot shows data with an arm-shaped enrichment.
volcanoplot
updated 2 days ago by
ATpoint
87k • written 2 days ago by
lea.preuss
• 0
0
votes
0
replies
135
views
Tool:
GENetLib: A Python Library for Gene–environment Interaction Analysis via Deep Learning
gene-environment
interaction
analysis
2 days ago by
Barry
• 0
9
votes
10
replies
487
views
STAR vs. Kallisto
STAR
kallisto
alignment
RNA-Seq
mapping
updated 2 days ago by
dsull
★ 7.4k • written 2 days ago by
gogeni5529
▴ 70
0
votes
0
replies
118
views
How to Annotate VCF with AlphaMissense Using VEP and dbNSFP v5.1a in Offline Mode?
AlphaMissense
dbNSFP
VEP
ensembl
2 days ago by
DareDevil
★ 4.4k
0
votes
1
reply
203
views
News:
Phylogenetic Comparative Methods in R (12–16 May, Online)
R
Phylogenetic-Comparative-Methods
updated 2 days ago by
Meeru
• 0 • written 3 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
191
views
Biostar handbook
Handbook
Biostar
updated 2 days ago by
GenoMax
151k • written 2 days ago by
himanshu0102
• 0
2
votes
2
replies
1.4k
views
pangenome - Create a diagram venn
roary
grep
awk
pangenome
venn
updated 2 days ago by
mplace
▴ 40 • written 2.0 years ago by
BATMAN
• 0
4
votes
4
replies
310
views
Addressing two nuisance factors in RNAseq
bulkRNAseq
updated 2 days ago by
ATpoint
87k • written 2 days ago by
jkim
▴ 190
0
votes
5
replies
340
views
DRAGEN FILTER
dragen
variant-calling
updated 3 days ago by
GenoMax
151k • written 3 days ago by
theresia.celine
• 0
0
votes
1
reply
305
views
Interpretation of the results: PCA
proteomics
PCA
updated 20 hours ago by
rfran010
★ 1.4k • written 3 days ago by
Ariadna
▴ 20
3
votes
5
replies
367
views
How to check normal BAM_files before create a Panel Of Normals (PoN)
GATK
variant_calling
PoN
3 days ago by
AIMAR
• 0
0
votes
1
reply
236
views
how to handle infinite M-values in methylation array data
M-value
methylation
infinite
array
updated 3 days ago by
Basti
★ 2.1k • written 3 days ago by
matt192
• 0
1
vote
3
replies
1.8k
views
Free and redistributable genomic data sets?
data
software-development
genomics
updated 3 days ago by
Meeru
• 0 • written 9.2 years ago by
woemler
▴ 170
2
votes
5
replies
1.1k
views
Rna-seq data
data
rna-seq
updated 3 days ago by
GenoMax
151k • written 3.2 years ago by
biology_inform
▴ 60
6
votes
3
replies
994
views
RNAseq example data
expression
RNA-Seq
data
next-gen
updated 3 days ago by
ehaag
▴ 20 • written 4.6 years ago by
rakinitopo
▴ 10
0
votes
1
reply
330
views
Transcript_id with "-0" after "flair collapse"
flair
updated 3 days ago by
GenoMax
151k • written 5 months ago by
anna_shin
• 0
0
votes
0
replies
175
views
Can I use glucose measured using two different devices in my study?
normalization
standardization
transformation
3 days ago by
Faith
▴ 50
1
vote
3
replies
723
views
Snakemake - pipeline shut down without error
snakemake
3 days ago by
bhumm
▴ 200
3
votes
2
replies
301
views
Source for `transcript_name` in GTFs
GTF
updated 3 days ago by
Jorge - Ensembl
▴ 30 • written 4 days ago by
gernophil
▴ 120
5
votes
5
replies
682
views
Tool:
Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
rad-seq
ddRADseq
demultiplexing
deduplication
4 days ago by
Rafal
▴ 10
0
votes
2
replies
239
views
How to normalised DNA sequencing depth for genomic variant discovery ?
normalisation
read-depth
variant-calling
updated 4 days ago by
Ram
45k • written 4 days ago by
AIMAR
• 0
2
votes
4
replies
345
views
RNASeq featureCounts Help Needed
fungi
featurecounts
RNASeq
4 days ago by
SomeOne
▴ 170
0
votes
0
replies
188
views
PAUP* error with exporting result file
PAUP
SVDquartet
4 days ago by
ylkim9
• 0
0
votes
1
reply
215
views
I need to convert Axiom output to PLINK format I did not find annotation.db
Axiom
PLINK
apt-format-result
updated 4 days ago by
GenoMax
151k • written 4 days ago by
AlmuhayyaA
• 0
1
vote
3
replies
344
views
How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
normalization
rna-seq
updated 3 days ago by
ATpoint
87k • written 4 days ago by
pipelinfections
• 0
1
vote
1
reply
289
views
Tool:
I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
python
pypi
updated 1 day ago by
Dunois
★ 2.9k • written 4 days ago by
Cris
▴ 10
0
votes
3
replies
391
views
Transcript ID
id
transcript
updated 4 days ago by
Meeru
• 0 • written 5 days ago by
cheong
• 0
0
votes
1
reply
262
views
Galaxy + RStudio
R
RNA-seq
RStudio
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
justus
• 0
8
votes
18
replies
3.2k
views
8 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 4 days ago by
jena
▴ 320 • written 20 months ago by
fishingline37
• 0
1
vote
2
replies
328
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 4 days ago by
dsull
★ 7.4k • written 5 days ago by
marc.zimmerli
▴ 10
0
votes
0
replies
229
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
5 days ago by
Tuấn Anh
• 0
2
votes
5
replies
735
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 5 days ago by
Darked89
4.7k • written 8 days ago by
Novoo
▴ 10
1
vote
1
reply
292
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 5 days ago by
ATpoint
87k • written 5 days ago by
Ariadna
▴ 20
1
vote
5
replies
478
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
updated 1 day ago by
Jordan M Eizenga
▴ 700 • written 5 days ago by
Pau
• 0
0
votes
0
replies
217
views
Dfam annotations
dfam
5 days ago by
frarodmar17
• 0
121,054 results • Page
1 of 2422
Recent Votes
No variant in the Pseudoautosomal regions of gomad chrY ?
Rna-seq data
Comment: Pre-Made STAR Index for mm10 Mouse Genome
Answer: Unable to find mitochondrial genes in latest rat genome(GRCr8)
How To Find The Pan Genome Of 30 Bacterial Strains
Current best practive to liftOver many SNVs from hg19 to GRCh38
Current best practive to liftOver many SNVs from hg19 to GRCh38
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Recent Replies
Comment: How to generate identiy score between aligned sequences with Mauve?
by
marongiu.luigi
▴ 740
Thank you, I used `[skani][1]` but it requires the build a model of several genomes together. Can I use it for only two genomes? [1]: …
Comment: How to generate identiy score between aligned sequences with Mauve?
by
marongiu.luigi
▴ 740
Thank you, I ran with `progressiveMauve --weight=15 --output=./out_file.mauve chr1.fa` where `chr1.fa` is a multifasta with the two genomes…
Answer: Genomic Data Portal (GDC) download a given a link file
by
bioinformagician
• 0
Solved using this, then merging all maf files into one. But would like a solution to download that one in specific just to check if it is t…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
GenoMax
151k
According to the manual a file is supposed to be produced by Mauve: https://darlinglab.org/mauve/user-guide/files.html#:~:text=The%20identi…
Answer: How to generate identiy score between aligned sequences with Mauve?
by
GenoMax
151k
`FastANI` has bee recommended by users here for this type of comparison (since you are mentioning `Mauve` you are likely referring to genom…
Comment: Cosmic database update issue in annovar
by
Ahmed
• 0
Ensure that the cosmic input files are not compressed. Also, Try using following prepare_annovar_user.pl: `http://www.openbioinformatics.o…
Answer: Cluster annotation in single cell
by
Shiyang
• 0
I'd like to recommend a new tool called **mLLMCelltype** that can greatly simplify the cluster annotation process for single-cell RNA-seq d…
Comment: Interpretation of the results: PCA
by
rfran010
★ 1.4k
I would say exact interpretations depend more on the nature of the data, experimental setup, and data processing steps. You provided some g…
Answer: Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under th
by
colindaven
7.4k
This might be very tricky. Try here https://sra-explorer.info/ Search for: ("Nicotiana benthamiana"[Organism] OR Nicotiana bent…
Comment: Pre-Made STAR Index for mm10 Mouse Genome
by
colindaven
7.4k
HiSat is another RNA-seq aligner which uses less RAM.
Comment: How to download the entire C. elegans genome from WormBase into Excel with autom
by
GenoMax
151k
Ah yes. I missed that button under step 2 on the query page.
Comment: How to download the entire C. elegans genome from WormBase into Excel with autom
by
Michael
55k
I'd just set the `download results as a tab-delimited file` radio button, and try to import the resulting tab-delimited file (about 8MB, no…
Comment: I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
by
Dunois
★ 2.9k
Firstly, nice work? That said, maybe I'm making a mountain out of a molehill but: > Tool:I packaged From [https://github.com/soda92/bowt…
Comment: Limma model gives weird results
by
SamGG
▴ 90
It is not clear to me how many samples (columns) are there in the `contig.abundance.table`. As the model is fitting 6 coefficients... `k…
Comment: Is vg toolkit suitable for haplotype calling?
by
Jordan M Eizenga
▴ 700
If your reads have errors that look similar to variants, you can certainly get alignment paths that correspond to non-biological transcript…
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