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121,919 results • Page
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Votes
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0
votes
2
replies
446
views
Help with species tree with orthofinder, iqtree and branch labeling
iqtree
trimal
CAFE5
orthofinder
mafft
updated 4 hours ago by
GenoMax
153k • written 15 hours ago by
san96
▴ 190
0
votes
0
replies
168
views
News:
In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 in Munich) - BS-Seq, ChIP-Seq, ATAC-Seq, ...
chip-seq
atac-seq
bs-seq
7 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
166
views
BWA alt-aware pipeline troubleshooting
alt-aware
BWA
samtools
7 hours ago by
Duy
• 0
0
votes
0
replies
148
views
News:
Last 3 seats: In-Person Single-Cell RNA-Seq Data Analysis Workshop (October 6-8 in Berlin)
scRNAseq
singleCell
transcriptomics
8 hours ago by
ecSeq Bioinformatics
▴ 20
845
votes
170
replies
209k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.6k • written 8.8 years ago by
Istvan Albert
103k
0
votes
3
replies
448
views
cellranger mkref fail/error
mkref
multiple_species
customtranscriptome
cellranger
transcriptome
updated 6 hours ago by
GenoMax
153k • written 8 hours ago by
tatsispolychronis
• 0
0
votes
2
replies
923
views
Methods to analyse structural similarity: co-evolution vs convergence
genomics
comparative
proteomics
evolutionary
updated 8 hours ago by
Joe
22k • written 1 day ago by
kelpotus22
• 0
3
votes
1
reply
280
views
vcf multisample
multi-sample
genomic
vcf
updated 9 hours ago by
Pierre Lindenbaum
166k • written 10 hours ago by
Donald
• 0
2
votes
4
replies
541
views
Genome Assembly QC from BAM files
QC
assembly
BAM
HiFi
7 hours ago by
SomeOne
▴ 240
0
votes
0
replies
627
views
News:
Last 2 Seats – Genome Assembly with Oxford Nanopore (29 Sept–3 Oct)
GenomeAssembly
Nanopore
longreads
1 day ago by
Physalia-courses
★ 2.6k
7
votes
9
replies
15k
views
8 follow
WGCNA package in R: dendogram plot error
wgcna
R
updated 1 day ago by
RJ
• 0 • written 8.7 years ago by
zyr123
▴ 40
7
votes
3
replies
5.1k
views
Different UMAP for batch correction in R and Pytho
harmony
UMAP
23 hours ago by
Madiha
▴ 20
0
votes
1
reply
2.9k
views
How to properly assemble phage genomes?
metagenomics
assembly
genome
virus
phage
updated 1 day ago by
Joe
22k • written 3 days ago by
marongiu.luigi
▴ 760
0
votes
1
reply
1.4k
views
Best set of tools / workflows for predicting the biosynthesis pathways of complex organic molecules
ngs
pathways
bioinformatics
updated 1 day ago by
Joe
22k • written 1 day ago by
Mark
▴ 60
0
votes
4
replies
2.4k
views
Forum:
Developing a genomics ML model using bytes?
Learning
Machine
Genomics
Bytes
updated 1 day ago by
dariober
15k • written 1 day ago by
Pranava
▴ 10
1
vote
4
replies
2.2k
views
miRNA low mapping ratings
mirna
bowtie1
preprocessing
counts
aligment
updated 11 hours ago by
i.sudbery
22k • written 1 day ago by
Ant
▴ 50
0
votes
4
replies
2.9k
views
Trouble when installing arb
arb
updated 1 day ago by
GenoMax
153k • written 2.9 years ago by
krmoon518
▴ 30
1
vote
0
replies
1.7k
views
News:
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
transcriptomics
RNAseq
2 days ago by
soledad.esteban
▴ 10
0
votes
0
replies
2.3k
views
rsid in full data table for GSA array but not in the final vcf file
array
GSA
3 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
2.7k
views
How to get a legend from genoplotR?
visualization
fastANI
genome
genoplotR
updated 1 day ago by
antonioggsousa
3.4k • written 3 days ago by
marongiu.luigi
▴ 760
0
votes
0
replies
2.6k
views
Custom reference sequence length discrepancy with STAR/Salmon/gffread
RefSeq
ENSEMBL
fasta
STAR
GTF
3 days ago by
ki
• 0
5
votes
5
replies
6.7k
views
Forum:
Tried building a compact sequence format with 4-bit storage
fasta
open-source
file-formats
data-storage
bioinformatics
updated 23 hours ago by
Alex Reynolds
36k • written 4 days ago by
Pranava
▴ 10
0
votes
1
reply
4.2k
views
Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio)
ontology
gene
updated 4 days ago by
GenoMax
153k • written 4 days ago by
Naveen
• 0
1
vote
5
replies
6.7k
views
STARlong for pacbio Isoseq reads
STARlong
STAR
pacbio
ISOSEQ
updated 4 days ago by
YuZJ
• 0 • written 4 days ago by
Buffo
★ 2.4k
0
votes
0
replies
3.0k
views
News:
online course: R/Bioconductor for Mass Spectrometry and Proteomics
R
MassSpectrometry
Proteomics
Bioconductor
4 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
3.5k
views
Subsetting before QC in Spatial Transcriptomics
spatial-transcriptomics
rare-cell-types
quality-control
4 days ago by
Kent
▴ 30
1
vote
4
replies
5.3k
views
Whole Genome Sequencing IG regions
immunoglobulin
wgs
updated 4 days ago by
GenoMax
153k • written 4 days ago by
719
• 0
1
vote
10
replies
6.9k
views
Hifiasm is getting killed while trying to assemble a genome
assembly
genome
hifiasm
updated 1 day ago by
GenoMax
153k • written 4 days ago by
pranavdatar01
• 0
0
votes
2
replies
5.4k
views
Transfer harmony-integrated scRNA-seq data to scanpy
scRNA-seq
harmony
updated 5 days ago by
Madiha
▴ 20 • written 24 months ago by
fifty_fifty
▴ 90
0
votes
0
replies
3.5k
views
News:
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Transcriptomic
analyses
updated 4 days ago by
GenoMax
153k • written 5 days ago by
soledad.esteban
▴ 10
0
votes
1
reply
4.1k
views
Pipeline for downloading, aligning, and curating influenza A and B sequences for primer design
Influenza
workflow
updated 5 days ago by
GenoMax
153k • written 5 days ago by
Mariano
• 0
3
votes
2
replies
5.6k
views
Shift in RNA 3' position, Term-Seq vs RNASeq
RNASeq
Bioinformatics
TermSeq
1 day ago by
npb27
▴ 20
0
votes
1
reply
4.3k
views
GTEx sQTL v8 – annotation version used?
qtl
gencode
sqtl
gtex
updated 5 days ago by
GenoMax
153k • written 5 days ago by
pedro.silvestre
• 0
1
vote
2
replies
5.0k
views
TCGA -derived Large RangeSummarizeExperient file
analysis
data
TCGA
updated 5 days ago by
ATpoint
89k • written 5 days ago by
Tom
• 0
3
votes
7
replies
8.0k
views
Yeast reference-based genome assembly
Reference
nanopore
yeast
genome
Assembly
updated 4 days ago by
colindaven
7.9k • written 6 days ago by
amy967107
• 0
0
votes
8
replies
7.3k
views
magpurify errors
magpurify
data
shotgun
updated 5 days ago by
GenoMax
153k • written 6 days ago by
shevch2009
▴ 20
0
votes
0
replies
4.4k
views
News:
online course: Population Genomics using aDNA Data
Paleogenomics
aDNA
PopulationGenomics
6 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
6.5k
views
Structural Variant identification on pangenome graphs
SV
variant
structural
graph
genome
5 days ago by
Panos
★ 1.8k
2
votes
2
replies
5.7k
views
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
ConsensusSequence
SequenceAlignment
ConservedMotifs
RNAi
TransposableElements
5 days ago by
manikin_python9f
▴ 20
23
votes
17
replies
37k
views
7 follow
Conversion of Gene Name to Ensembl ID
gene
RNA-Seq
R
genome
updated 6 days ago by
Thanujay S
• 0 • written 5.5 years ago by
bazok
▴ 40
1
vote
5
replies
6.0k
views
Variant analysis for mouse WES
variant-calling
maftools
vcf
genome
wes
updated 6 days ago by
GenoMax
153k • written 6 days ago by
alba
• 0
6
votes
4
replies
7.7k
views
Is this PCA plot correct??
PCA
updated 6 days ago by
GenoMax
153k • written 7 days ago by
m00nphany
• 0
0
votes
0
replies
4.7k
views
metabolite identification related issue
metabolomics
metaboanalyst
6 days ago by
abhisekde038
• 0
0
votes
1
reply
5.2k
views
Strange pattern in pct_counts_mt from bin2cell deconvolved VisiumHD data
spatial-transcriptomics
bin2cell
VisiumHD
6 days ago by
danielpintard
▴ 10
0
votes
2
replies
5.6k
views
Forum:
Splice junctions plots for long-read seq data
splice-junctions
alternative-splicing
long-read-sequencing
2 days ago by
alison.ludzki
• 0
0
votes
0
replies
5.0k
views
News:
Introduction to Nextflow course - online, 10–12 November
Pipeline
NGSdata
Nextflow
Reproducibility
Workflow-Manager
7 days ago by
Physalia-courses
★ 2.6k
33
votes
21
replies
34k
views
12 follow
Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
ensembl
ucsc
genome
mapping
coordinates
updated 6 days ago by
Thanujay S
• 0 • written 13.9 years ago by
Ryan D
★ 3.4k
3
votes
4
replies
6.6k
views
How to debug faulty BBmap clumpify command?
bbmap
fastq
trimming
genome
4 days ago by
marongiu.luigi
▴ 760
1
vote
3
replies
6.7k
views
Best way to do protein structure guided similarity search?
alphafold
BLAST
structure
proteins
updated 7 days ago by
Dunois
★ 2.9k • written 7 days ago by
Mark
▴ 60
0
votes
1
reply
5.5k
views
Finding RNA genes associated with X protein expression in CITE-seq Seurat object
seq
cite
single
cell
updated 7 days ago by
ATpoint
89k • written 7 days ago by
Picasa
▴ 690
121,919 results • Page
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Recent Votes
A: Binning Over Genes And Calculating The Coverage [Bedops/Bedmap]
Answer: [vg giraffe] Unable to add read group to BAM file
Comment: [vg giraffe] Unable to add read group to BAM file
Answer: [vg giraffe] Unable to add read group to BAM file
Answer: vcf multisample
Answer: vcf multisample
Answer: vcf multisample
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Recent Replies
Comment: Help with species tree with orthofinder, iqtree and branch labeling
by
GenoMax
153k
> I don’t have clear species labels in my headers, only sequence IDs. I have not used iqtree, so this is only a thought ... should it be y…
Comment: Help with species tree with orthofinder, iqtree and branch labeling
by
san96
▴ 190
Thank you so much.
Comment: [vg giraffe] Unable to add read group to BAM file
by
saruman
▴ 10
Yes, it seems so. Thank you.
Comment: cellranger mkref fail/error
by
GenoMax
153k
> The thing is that I do not have a genome for these organisms. That is not what `cellranger mkref` is expecting. You could consider alt…
Comment: cellranger mkref fail/error
by
tatsispolychronis
• 0
The thing is that I do not have a genome for these organisms. i made a transcriptome using TRinity and this is what I am feeding it. I do n…
Comment: Genome Assembly QC from BAM files
by
SomeOne
▴ 240
Hi, I am not sure if i can call them good assemblies. Although based on QUAST and BUSCO stats, everything looks too good but somehow i hav…
Comment: cellranger mkref fail/error
by
GenoMax
153k
You need to provide the genome reference for the `--fasta` option as noted in https://www.10xgenomics.com/support/software/cell-ranger/late…
Answer: Methods to analyse structural similarity: co-evolution vs convergence
by
Joe
22k
Without historical data (ancient DNA) there's no way to ever really know this for certain. The best we can do is make inferences based on t…
Answer: vcf multisample
by
Pierre Lindenbaum
166k
eg : https://ega-archive.org/datasets/EGAD50000001683 > Merged VCF file from sporadic Meniere disease cohort (found using https://dat…
Comment: Genome Assembly QC from BAM files
by
GenoMax
153k
Since this saga has been on going for a long time, it will be helpful to add a comment as to how you finally got to this point of what seem…
Comment: Methods to analyse structural similarity: co-evolution vs convergence
by
dthorbur
★ 3.1k
A few comments. 1. Coevolution of a trait between 2 organisms can end up with a convergent structure with another organism. It's not e…
Comment: Genome Assembly QC from BAM files
by
SomeOne
▴ 240
Thank you. Based on the description these two look really what i wanted to see.
Comment: miRNA low mapping ratings
by
i.sudbery
22k
Also, can you just clarify that the output above is from cutadapt or form miRDeep2?
Comment: miRNA low mapping ratings
by
i.sudbery
22k
What happens if you remove the `--minimum-length` requirement to cutadapt, and then run fastqc on the result - what size disitribution do y…
Answer: Genome Assembly QC from BAM files
by
colindaven
7.9k
You can have a look at the tools in the PAQman pipeline https://github.com/SAMtoBAM/PAQman, and maybe also Inspector https://github.com/Mag…
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