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113,876 results • Page
1 of 2278
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0
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0
replies
4
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How to identify CG, CHG, or CHH from MeDIP data
CHG
software
CHH
CG
MeDIP
just now by
Tm
★ 1.1k
0
votes
1
reply
88
views
GO categorization
Ontology
Gene
updated 20 minutes ago by
Istvan Albert
99k • written 17 hours ago by
m.habib
• 0
0
votes
0
replies
19
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
1 hour ago by
CoLa
• 0
0
votes
0
replies
39
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
2 hours ago by
ManuelDB
▴ 80
0
votes
4
replies
100
views
Problematic fastq files...How can we trust them?
fastq
updated just now by
Istvan Albert
99k • written 3 hours ago by
blackadder
▴ 30
0
votes
3
replies
105
views
An incomprehensible error with R package gggenes
R
gggenes
visualize
updated 3 hours ago by
ATpoint
78k • written 4 hours ago by
alice005201314
• 0
772
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
1
reply
116
views
Should I scale all genes in single cell Seurat?
singlecell
updated 5 hours ago by
antonioggsousa
3.0k • written 21 hours ago by
synat.keam
▴ 80
0
votes
1
reply
55
views
doubt about usage of megahit
trinity
megahit
updated 30 minutes ago by
Istvan Albert
99k • written 7 hours ago by
meera
• 0
0
votes
0
replies
48
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
7 hours ago by
Peerzada
• 0
0
votes
1
reply
102
views
DIAMOND tutorial
tutorial
DIAMOND
updated 10 hours ago by
GenoMax
136k • written 12 hours ago by
sooni
▴ 10
0
votes
13
replies
891
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling
chromium
cellranger
scFFPE
updated 12 hours ago by
MohammadAlkadi
▴ 70 • written 5 weeks ago by
bk11
★ 1.8k
0
votes
2
replies
180
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic
bioinformatic
updated 13 hours ago by
Kevin Blighe
86k • written 19 hours ago by
Giovana
• 0
2
votes
8
replies
648
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 15 hours ago by
ATpoint
78k • written 19 days ago by
ellen.francis
▴ 10
0
votes
0
replies
71
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
15 hours ago by
O.rka
▴ 710
0
votes
1
reply
367
views
Loftee no splice site annotations
Loftee
VEP
updated 16 hours ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
1
vote
1
reply
139
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq
bulk_RNA-seq
online_course
updated 17 hours ago by
swbarnes2
13k • written 22 hours ago by
ire
• 0
0
votes
1
reply
99
views
gene set enrichment analysis- by enrichGO
rna-seq
GO
enrichment
updated 17 hours ago by
Istvan Albert
99k • written 17 hours ago by
CL
• 0
0
votes
0
replies
61
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
17 hours ago by
luckyday1661
• 0
0
votes
1
reply
95
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 10 hours ago by
GenoMax
136k • written 17 hours ago by
Nicolas
• 0
0
votes
0
replies
79
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
15 hours ago by
Ty
• 0
0
votes
1
reply
95
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 3 hours ago by
cmdcolin
★ 3.4k • written 19 hours ago by
Trevor
• 0
0
votes
0
replies
76
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
20 hours ago by
bioinfo
▴ 140
0
votes
1
reply
133
views
Where do these snpeff annotation come from?
snpeff
updated 20 hours ago by
Istvan Albert
99k • written 23 hours ago by
curious
▴ 730
3
votes
4
replies
241
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
12 hours ago by
CTLong
▴ 20
4
votes
5
replies
852
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 21 hours ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
0
votes
3
replies
190
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 21 hours ago by
Istvan Albert
99k • written 1 day ago by
Jingfang
• 0
3
votes
2
replies
332
views
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
SNP
bbtools
updated 18 hours ago by
harold.smith.tarheel
★ 4.9k • written 1 day ago by
Axzd
▴ 50
0
votes
1
reply
88
views
News:
Course: Genome Assembly and Annotation
GenomeAssembly
GenomeAnnotation
Longreads
Bioinformatics
Biodiversity
updated 23 hours ago by
sil_bioinfo
▴ 30 • written 23 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
215
views
How I add new organism "Beauveria bassiana (strain ARSEF 2860)" in ClueGo plug-in of cytoscape?
cytoscape
updated 23 hours ago by
Scooter
▴ 180 • written 26 days ago by
A
• 0
0
votes
1
reply
251
views
Gene Ontology enrichment with BINGO and ClueGO
BINGO
Cytoscape
ClueGO
Gene
Ontology
updated 23 hours ago by
Scooter
▴ 180 • written 14 days ago by
David R
▴ 20
0
votes
1
reply
171
views
String App in Cytoscape
App
String
cytoscape
updated 23 hours ago by
Scooter
▴ 180 • written 3 days ago by
hellokwmin
• 0
5
votes
8
replies
359
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
59 minutes ago by
sil_bioinfo
▴ 30
0
votes
1
reply
121
views
Salmon indices differences
salmon
RNAseq
index
refgenie
decoy
updated 1 day ago by
ATpoint
78k • written 1 day ago by
enee
▴ 10
3
votes
2
replies
260
views
Mapping quality in `vg giraffe`
vg
1 day ago by
Wenhai
• 0
0
votes
1
reply
131
views
PAML Troubleshooting Help
PAML
codeml
updated 23 hours ago by
dthorbur
▴ 890 • written 1 day ago by
sebabiokr
▴ 10
0
votes
4
replies
213
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 1 day ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
abourrieau
• 0
0
votes
0
replies
85
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
1 day ago by
hellokwmin
• 0
2
votes
2
replies
189
views
R script in docker
R
Visual_studio_code
Docker
23 hours ago by
mrashad
▴ 70
2
votes
3
replies
186
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 1 day ago by
Basti
★ 1.9k • written 1 day ago by
CTLong
▴ 20
0
votes
0
replies
79
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
1 day ago by
maxlaubstein
• 0
0
votes
3
replies
172
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
1 day ago by
J
• 0
0
votes
3
replies
195
views
ERROR FILE EXTENSION
Prokka
1 day ago by
syirah4
• 0
0
votes
1
reply
147
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
updated 1 day ago by
Tao
▴ 30 • written 1 day ago by
Bryan
▴ 10
0
votes
9
replies
445
views
Where is the index command?
samtools
updated 1 day ago by
Michael
53k • written 1 day ago by
luque007
• 0
0
votes
0
replies
109
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
1 day ago by
luckyday1661
• 0
0
votes
2
replies
218
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 1 day ago by
fracarb8
★ 1.3k • written 1 day ago by
synat.keam
▴ 80
0
votes
0
replies
96
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
1 day ago by
DINESHR
• 0
3
votes
5
replies
342
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 3 hours ago by
rpolicastro
12k • written 1 day ago by
newbee
▴ 40
0
votes
0
replies
114
views
deeptools k-means clustering
heatmap
deeptools
chipseq
1 day ago by
biology_inform
▴ 50
113,876 results • Page
1 of 2278
Recent Votes
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Answer: 1000 genomes project reference panel - GRCh38
Answer: 1000 genomes project reference panel - GRCh38
Comment: IMPUTE2- Map file for custom reference panel
IMPUTE2- Map file for custom reference panel
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Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
jucosie
• 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$dir_c…
Comment: Problematic fastq files...How can we trust them?
by
Istvan Albert
99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization
by
Istvan Albert
99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
Comment: doubt about usage of megahit
by
Istvan Albert
99k
you have not mentioned what kind of resources you have, how much data you have to process and what the expected genome/transcriptome sizes …
Comment: Problematic fastq files...How can we trust them?
by
ATpoint
78k
Then tell her to bring proper data. In the lab you also don't use buffers with mold growing in it, and in bioinformatics we don't start wit…
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Its not my data. An external researcher is visiting and she wanted from us to do some bioinformatics... The samples were not sequenced by u…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
Oh, I understand. Thank you so much for your help! The truth is that there is so much information, so many packages, libraries, tutorials,…
Comment: Tools or R / Python packages to perfom ML models
by
Matthias Zepper
4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
Answer: Problematic fastq files...How can we trust them?
by
ATpoint
78k
> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
They could have saved themselves a ton of money by sequencing this on a miseq.
Comment: Annotate Unplaced Scaffold with Chromosome Information
by
cmdcolin
★ 3.4k
I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
Comment: An incomprehensible error with R package gggenes
by
ATpoint
78k
It's not stupid, just a bit lazy ;-)
Comment: Adding functional annotation and meta-data of MAKER/BRAKER GFF
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ben@f
• 0
Hi, did you find an effective solution for this problem? beside Agat and
Comment: An incomprehensible error with R package gggenes
by
alice005201314
• 0
Thank you. I asked a stupid question.
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