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116,470 results • Page
1 of 2330
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python file for cpc2
cpc2.py
just now by
Ashok
• 0
0
votes
0
replies
5
views
error in CPC2
cpc
CPC2
potential
coding
5 minutes ago by
Ashok
• 0
0
votes
0
replies
5
views
miRNAs quantification using mirdeep2 tool
differential
expression
mirdeep2
analysis
miRNA
10 minutes ago by
Ashok
• 0
1
vote
1
reply
66
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
iamsmor
• 0
2
votes
2
replies
220
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 3 hours ago by
shelkmike
★ 1.2k • written 11 hours ago by
kirillkirilenko
▴ 30
0
votes
0
replies
42
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 3 hours ago by
Ram
43k • written 3 hours ago by
samuelkalandarov2002
• 0
1
vote
1
reply
184
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
4 hours ago by
otieno43
▴ 30
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
95
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 3 hours ago by
Ram
43k • written 3 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
44
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 4 hours ago by
Ram
43k • written 4 hours ago by
Javier
• 0
1
vote
4
replies
536
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 4 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
40
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
4 hours ago by
enferdeflame
• 0
0
votes
0
replies
48
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
14 minutes ago by
Chris
▴ 260
0
votes
0
replies
56
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 4 hours ago by
Ram
43k • written 6 hours ago by
carlopecoraro2
★ 2.5k
1
vote
9
replies
545
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 6 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 11 hours ago by
Jacky
• 0
0
votes
1
reply
137
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 7 hours ago by
GenoMax
141k • written 8 hours ago by
predeus
★ 1.9k
0
votes
1
reply
147
views
DEseq2
RNA-seq
DESeq2
updated 4 hours ago by
Ram
43k • written 9 hours ago by
rrehimi
• 0
0
votes
0
replies
60
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 4 hours ago by
Ram
43k • written 8 hours ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
202
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 8 hours ago by
Juke34
8.5k • written 9 hours ago by
njornet
▴ 20
0
votes
0
replies
61
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
9 hours ago by
Novogene
▴ 410
0
votes
1
reply
353
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 4 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
2
replies
211
views
Korean human genome reference file
GWAS
reference
imputation
updated 7 hours ago by
GenoMax
141k • written 11 hours ago by
SeoGyun
• 0
1
vote
4
replies
309
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 7 hours ago by
GenoMax
141k • written 10 hours ago by
n_navy
• 0
0
votes
2
replies
190
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 4 hours ago by
Ram
43k • written 10 hours ago by
rrehimi
• 0
0
votes
0
replies
66
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 4 hours ago by
Ram
43k • written 11 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
76
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
11 hours ago by
P.
• 0
0
votes
0
replies
80
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
13 hours ago by
ekirsch
• 0
0
votes
0
replies
113
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
18 hours ago by
renan.igor
• 0
1
vote
1
reply
175
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 14 hours ago by
Ram
43k • written 20 hours ago by
anasjamshed
▴ 120
3
votes
1
reply
544
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 19 hours ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
99
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
20 hours ago by
synat.keam
▴ 100
0
votes
1
reply
188
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 22 hours ago by
GenoMax
141k • written 22 hours ago by
ycts
• 0
2
votes
3
replies
384
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 23 hours ago by
swbarnes2
14k • written 1 day ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
214
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 1 day ago by
LChart
3.9k • written 1 day ago by
George
▴ 10
0
votes
3
replies
285
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 1 hour ago by
GenoMax
141k • written 1 day ago by
Kai Xin
• 0
1
vote
1
reply
175
views
Retrieve a % coverage for each transcript
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
jammydodger123456
▴ 40
0
votes
1
reply
295
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 1 day ago by
Klaus S
▴ 150 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
269
views
How can I solve this error?
metal
16 hours ago by
22211020193
• 0
0
votes
0
replies
109
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 1 day ago by
GenoMax
141k • written 1 day ago by
srimmer
• 0
1
vote
2
replies
209
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 1 day ago by
Ram
43k • written 1 day ago by
aniigodwinn
• 0
2
votes
3
replies
297
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
6 hours ago by
valentinatsar
• 0
1
vote
3
replies
220
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 1 day ago by
Michael
54k • written 1 day ago by
LDT
▴ 330
1
vote
10
replies
521
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 4 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
2
votes
2
replies
298
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
3 hours ago by
nhaus
▴ 300
0
votes
0
replies
201
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
1 day ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
6
replies
554
views
Removing duplicates
duplicates
ONT
minimap2
11 hours ago by
quentinperriere
• 0
0
votes
1
reply
152
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 1 day ago by
DKA
▴ 40 • written 1 day ago by
james.melhorn
• 0
3
votes
4
replies
308
views
biomaRt error for different R version
biomaRt
R
updated 7 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
0
votes
1
reply
142
views
Freyja plot error
Freyja
updated 1 day ago by
Ram
43k • written 1 day ago by
Adyasha
• 0
116,470 results • Page
1 of 2330
Recent Votes
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
Comment: Downloaded pdb's on rcsb.org
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
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141k
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jkbonfield
★ 1.2k
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▴ 250
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▴ 110
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Recent Replies
Comment: Per base sequence content failed miserably
by
GenoMax
141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ?
by
kjngo
• 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies
by
shelkmike
★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
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