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121,908 results • Page
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News:
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
transcriptomics
RNAseq
12 hours ago by
soledad.esteban
▴ 10
0
votes
0
replies
1.1k
views
rsid in full data table for GSA array but not in the final vcf file
array
GSA
1 day ago by
1769mkc
★ 1.3k
0
votes
0
replies
1.2k
views
How to get a legend from genoplotR?
visualization
fastANI
genome
genoplotR
1 day ago by
marongiu.luigi
▴ 760
0
votes
0
replies
1.2k
views
How to properly assemble phage genomes?
metagenomics
assembly
genome
virus
phage
1 day ago by
marongiu.luigi
▴ 760
845
votes
170
replies
208k
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
0
replies
1.3k
views
Custom reference sequence length discrepancy with STAR/Salmon/gffread
RefSeq
ENSEMBL
fasta
STAR
GTF
1 day ago by
ki
• 0
4
votes
4
replies
4.1k
views
Forum:
Tried building a compact sequence format with 4-bit storage
fasta
open-source
file-formats
data-storage
bioinformatics
15 hours ago by
Pranava
▴ 10
0
votes
1
reply
2.7k
views
Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio)
ontology
gene
updated 1 day ago by
GenoMax
153k • written 1 day ago by
Naveen
• 0
1
vote
5
replies
5.2k
views
STARlong for pacbio Isoseq reads
STARlong
STAR
pacbio
ISOSEQ
updated 1 day ago by
YuZJ
• 0 • written 2 days ago by
Buffo
★ 2.4k
0
votes
0
replies
1.8k
views
News:
online course: R/Bioconductor for Mass Spectrometry and Proteomics
R
MassSpectrometry
Proteomics
Bioconductor
2 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
2.2k
views
Subsetting before QC in Spatial Transcriptomics
spatial-transcriptomics
rare-cell-types
quality-control
2 days ago by
Kent
▴ 30
1
vote
4
replies
3.8k
views
Whole Genome Sequencing IG regions
immunoglobulin
wgs
updated 1 day ago by
GenoMax
153k • written 2 days ago by
719
• 0
1
vote
8
replies
4.0k
views
Hifiasm is getting killed while trying to assemble a genome
assembly
genome
hifiasm
2 hours ago by
pranavdatar01
• 0
0
votes
2
replies
4.2k
views
Transfer harmony-integrated scRNA-seq data to scanpy
scRNA-seq
harmony
updated 2 days ago by
Madiha
▴ 10 • written 24 months ago by
fifty_fifty
▴ 90
0
votes
0
replies
2.3k
views
News:
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Transcriptomic
analyses
updated 2 days ago by
GenoMax
153k • written 2 days ago by
soledad.esteban
▴ 10
0
votes
1
reply
2.8k
views
Pipeline for downloading, aligning, and curating influenza A and B sequences for primer design
Influenza
workflow
updated 2 days ago by
GenoMax
153k • written 2 days ago by
Mariano
• 0
1
vote
1
reply
3.6k
views
Shift in RNA 3' position, Term-Seq vs RNASeq
RNASeq
Bioinformatics
TermSeq
updated 1 day ago by
acvill
▴ 350 • written 3 days ago by
npb27
▴ 10
1
vote
1
reply
3.0k
views
Different UMAP for batch correction in R and Pytho
harmony
UMAP
2 days ago by
Madiha
▴ 10
0
votes
1
reply
3.1k
views
GTEx sQTL v8 – annotation version used?
qtl
gencode
sqtl
gtex
updated 3 days ago by
GenoMax
153k • written 3 days ago by
pedro.silvestre
• 0
1
vote
2
replies
3.8k
views
TCGA -derived Large RangeSummarizeExperient file
analysis
data
TCGA
updated 3 days ago by
ATpoint
89k • written 3 days ago by
Tom
• 0
3
votes
7
replies
6.8k
views
Yeast reference-based genome assembly
Reference
nanopore
yeast
genome
Assembly
updated 2 days ago by
colindaven
7.9k • written 4 days ago by
amy967107
• 0
0
votes
8
replies
6.1k
views
magpurify errors
magpurify
data
shotgun
updated 3 days ago by
GenoMax
153k • written 4 days ago by
shevch2009
▴ 20
0
votes
0
replies
3.2k
views
News:
online course: Population Genomics using aDNA Data
Paleogenomics
aDNA
PopulationGenomics
4 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
5.2k
views
Structural Variant identification on pangenome graphs
SV
variant
structural
graph
genome
3 days ago by
Panos
★ 1.8k
2
votes
2
replies
4.4k
views
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
ConsensusSequence
SequenceAlignment
ConservedMotifs
RNAi
TransposableElements
3 days ago by
manikin_python9f
▴ 20
23
votes
17
replies
35k
views
7 follow
Conversion of Gene Name to Ensembl ID
gene
RNA-Seq
R
genome
updated 4 days ago by
Thanujay S
• 0 • written 5.5 years ago by
bazok
▴ 40
0
votes
5
replies
4.7k
views
Variant analysis for mouse WES
variant-calling
maftools
vcf
genome
wes
updated 3 days ago by
GenoMax
153k • written 4 days ago by
alba
• 0
6
votes
4
replies
6.5k
views
Is this PCA plot correct??
PCA
updated 4 days ago by
GenoMax
153k • written 4 days ago by
m00nphany
• 0
0
votes
0
replies
3.6k
views
metabolite identification related issue
metabolomics
metaboanalyst
4 days ago by
abhisekde038
• 0
0
votes
1
reply
3.9k
views
Strange pattern in pct_counts_mt from bin2cell deconvolved VisiumHD data
spatial-transcriptomics
bin2cell
VisiumHD
4 days ago by
danielpintard
▴ 10
0
votes
2
replies
4.1k
views
Forum:
Splice junctions plots for long-read seq data
splice-junctions
alternative-splicing
long-read-sequencing
19 hours ago by
alison.ludzki
• 0
0
votes
0
replies
3.8k
views
News:
Introduction to Nextflow course - online, 10–12 November
Pipeline
NGSdata
Nextflow
Reproducibility
Workflow-Manager
5 days ago by
Physalia-courses
★ 2.6k
33
votes
21
replies
33k
views
12 follow
Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
ensembl
ucsc
genome
mapping
coordinates
updated 4 days ago by
Thanujay S
• 0 • written 13.9 years ago by
Ryan D
★ 3.4k
3
votes
4
replies
5.4k
views
How to debug faulty BBmap clumpify command?
bbmap
fastq
trimming
genome
2 days ago by
marongiu.luigi
▴ 760
1
vote
3
replies
5.4k
views
Best way to do protein structure guided similarity search?
alphafold
BLAST
structure
proteins
updated 4 days ago by
Dunois
★ 2.9k • written 5 days ago by
Mark
▴ 60
0
votes
1
reply
4.3k
views
Finding RNA genes associated with X protein expression in CITE-seq Seurat object
seq
cite
single
cell
updated 5 days ago by
ATpoint
89k • written 5 days ago by
Picasa
▴ 690
1
vote
5
replies
5.2k
views
Need help in Single cell proteomics data analysis
single
cell
updated 5 days ago by
ATpoint
89k • written 5 days ago by
Saber_J
▴ 20
5
votes
2
replies
5.4k
views
Fastq reads to csv - How can I make a csv with the read number of several fastq files in the same folder?
illumina
csv
read
fastq
count
updated 5 days ago by
GenoMax
153k • written 5 days ago by
alx.alo
• 0
1
vote
3
replies
5.3k
views
Mapping amplicon to a reference sequence with iteration / elongation
Barcoding
NGS
Mapping
updated 5 days ago by
mmahe
• 0 • written 4.4 years ago by
marion.couedel
▴ 10
0
votes
1
reply
4.8k
views
MERLIN haplotyping
MERLIN
updated 5 days ago by
Prashant
• 0 • written 3.2 years ago by
smb2174
▴ 20
0
votes
0
replies
4.4k
views
Radial plot help
Radial-Plots
Bulls-eye
updated 5 days ago by
Ram
45k • written 5 days ago by
bioinformatics_rk
▴ 10
1
vote
1
reply
4.8k
views
dbSNP VCF file compatible with GRch38.p14
vcf
samtools
updated 5 days ago by
GenoMax
153k • written 5 days ago by
Kelly
• 0
0
votes
0
replies
4.6k
views
News:
Single-Cell RNA-Seq Analysis
RNA-seq
Single
cell
updated 6 days ago by
GenoMax
153k • written 6 days ago by
oliverhooker
▴ 110
0
votes
0
replies
4.5k
views
News:
Introduction to Snakemake
Snakemake
updated 6 days ago by
GenoMax
153k • written 6 days ago by
oliverhooker
▴ 110
0
votes
0
replies
4.5k
views
News:
course - Introduction to Deep Learning for Biologists -Online, 3–7 November
MachineLearning
Python
ConvolutionalNeuralNetwork
DeepLearning
6 days ago by
Physalia-courses
★ 2.6k
1
vote
7
replies
11k
views
6 follow
Low Mapping Rate with Kallisto on RNA-seq Data
RNAseq
mapping
ratio
kallisto
low
updated 5 days ago by
dsull
★ 7.7k • written 12 days ago by
meetmet
▴ 10
5
votes
6
replies
10k
views
Is total miRNA in EV constant? Implications for library size normalization.
rna-seq
updated 1 day ago by
Gordon Smyth
★ 8.3k • written 8 days ago by
Thomas.H.Hampton
▴ 10
1
vote
4
replies
6.0k
views
single cell: differential expression between cluster subsets
scrna-seq
statistics
seurat
5 days ago by
Lee
• 0
1
vote
0
replies
4.7k
views
Tool:
evorca: fast and minimal plmDCA in JAX
jax
python
protein-contact-prediction
bioinformatics
plmdca
6 days ago by
Shosuke
▴ 10
2
votes
9
replies
6.8k
views
6 follow
How to load sam.gz files on IGV?
visualization
genome
IGV
mapping
updated 6 days ago by
GenoMax
153k • written 6 days ago by
marongiu.luigi
▴ 760
121,908 results • Page
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GSEA vs GO enrichment
Blastn and Kraken2 short reads clssification
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
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soledad.esteban
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Recent Replies
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
• 0
Yes, I did check for adaptor contamination, and did not find any. I have kept all the reads with quality score of more than 30.
Comment: Hifiasm is getting killed while trying to assemble a genome
by
Panos
★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage
by
Pranava
▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data
by
alison.ludzki
• 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
• 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage
by
Alex Reynolds
36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
Panos
★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization.
by
Gordon Smyth
★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage
by
Pranava
▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage
by
Matthias Zepper
5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio)
by
GenoMax
153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions
by
GenoMax
153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest
by
piffelpaff
• 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads
by
YuZJ
• 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq
by
acvill
▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
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