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116,472 results • Page
1 of 2330
Sort: Rank
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Votes
Replies
6
votes
7
replies
152
views
Downloaded pdb's on rcsb.org
rcsb
pdb
2 minutes ago by
iamsmor
• 0
0
votes
0
replies
12
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
13 minutes ago by
rahu
• 0
0
votes
0
replies
24
views
create genewise sync file in popoolation
popoolation
updated 10 minutes ago by
GenoMax
141k • written 1 hour ago by
N.Y.Wiyana-Hewage
• 0
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
2
replies
69
views
python file for cpc2
cpc2.py
updated 1 hour ago by
Ram
43k • written 1 hour ago by
Ashok
• 0
0
votes
2
replies
61
views
error in CPC2
cpc
CPC2
coding-potential
updated 1 hour ago by
Ram
43k • written 1 hour ago by
Ashok
• 0
0
votes
1
reply
23
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
updated just now by
GenoMax
141k • written 1 hour ago by
Ashok
• 0
2
votes
2
replies
246
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 5 hours ago by
shelkmike
★ 1.2k • written 12 hours ago by
kirillkirilenko
▴ 30
0
votes
0
replies
49
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 5 hours ago by
Ram
43k • written 5 hours ago by
samuelkalandarov2002
• 0
1
vote
1
reply
200
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
5 hours ago by
otieno43
▴ 30
0
votes
1
reply
111
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 5 hours ago by
Ram
43k • written 5 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
52
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 6 hours ago by
Ram
43k • written 6 hours ago by
Javier
• 0
1
vote
4
replies
550
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 6 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
48
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
6 hours ago by
enferdeflame
• 0
0
votes
0
replies
55
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
1 hour ago by
Chris
▴ 260
0
votes
0
replies
61
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 6 hours ago by
Ram
43k • written 8 hours ago by
carlopecoraro2
★ 2.5k
1
vote
9
replies
558
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 8 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 12 hours ago by
Jacky
• 0
0
votes
1
reply
145
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 9 hours ago by
GenoMax
141k • written 10 hours ago by
predeus
★ 1.9k
0
votes
1
reply
153
views
DEseq2
RNA-seq
DESeq2
updated 6 hours ago by
Ram
43k • written 11 hours ago by
rrehimi
• 0
0
votes
0
replies
64
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 6 hours ago by
Ram
43k • written 9 hours ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
214
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 10 hours ago by
Juke34
8.5k • written 10 hours ago by
njornet
▴ 20
0
votes
0
replies
66
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
10 hours ago by
Novogene
▴ 410
0
votes
1
reply
356
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 6 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
2
replies
216
views
Korean human genome reference file
GWAS
reference
imputation
updated 8 hours ago by
GenoMax
141k • written 12 hours ago by
SeoGyun
• 0
1
vote
4
replies
319
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 8 hours ago by
GenoMax
141k • written 12 hours ago by
n_navy
• 0
0
votes
2
replies
197
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 6 hours ago by
Ram
43k • written 12 hours ago by
rrehimi
• 0
0
votes
0
replies
71
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 6 hours ago by
Ram
43k • written 13 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
80
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
13 hours ago by
P.
• 0
0
votes
0
replies
86
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
15 hours ago by
ekirsch
• 0
0
votes
0
replies
117
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
20 hours ago by
renan.igor
• 0
1
vote
1
reply
178
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 16 hours ago by
Ram
43k • written 22 hours ago by
anasjamshed
▴ 120
3
votes
1
reply
549
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 21 hours ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
102
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
22 hours ago by
synat.keam
▴ 100
0
votes
1
reply
192
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
ycts
• 0
5
votes
4
replies
417
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
1 hour ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
219
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
316
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 2 hours ago by
GenoMax
141k • written 1 day ago by
Kai Xin
• 0
1
vote
1
reply
177
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
298
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
277
views
How can I solve this error?
metal
18 hours ago by
22211020193
• 0
0
votes
0
replies
112
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
213
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
312
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
8 hours ago by
valentinatsar
• 0
1
vote
3
replies
224
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
2
votes
10
replies
539
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 5 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
2
votes
2
replies
316
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
5 hours ago by
nhaus
▴ 300
0
votes
0
replies
211
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
567
views
Removing duplicates
duplicates
ONT
minimap2
13 hours ago by
quentinperriere
• 0
0
votes
1
reply
156
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
116,472 results • Page
1 of 2330
Recent Votes
Answer: Bedtools nuc : calculating the GC content in a sliding window
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Comment: Questions about a bug when transferring cram file to bam file
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
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Recent Replies
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
great guidance ... thank you
Comment: error in CPC2
by
Ram
43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2
by
Ram
43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Comment: python file for cpc2
by
Pierre Lindenbaum
161k
https://academic.oup.com/nar/article/45/W1/W12/3831091 > CPC2: a fast and accurate coding potential calculator based on sequence intrinsic…
Comment: error in CPC2
by
GenoMax
141k
Looks like you are running code that was written for `python v.2.x` but you probably have `python v.3.x` or a newer version than `python v.…
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.
Answer: 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 …
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