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News: online course: Efficient Data Analysis with data.table in R - 8 October
R Programming DataTable
17 days ago by Physalia-courses ★ 2.7k
1
vote
0
replies
674
views
Tool: Modernized RNA-MuTect pipeline for tumor-only RNA-seq somatic variant calling
somatic rna-seq
17 days ago by darklings ▴ 590
0
votes
4
replies
2.3k
views
pySCENIC aucell matrix is all 0s
CLI SCENIC grn aucell
17 days ago by Tripfantasy • 0
1
vote
1
reply
824
views
Slam-Seq Conversion Rate per Read
nf-core slam-seq slamdunk
updated 17 days ago by ★ 4.0k • written 17 days ago by ▴ 40
2
votes
1
reply
1.3k
views
MAPQ algorithms of Giraffe
giraffe vg
updated 17 days ago by ▴ 180 • written 4 months ago by • 0
1
vote
0
replies
765
views
Job: Bioinformatician, Senior Research Associate STS
omics jobs hiring bioinformatics
17 days ago by William ▴ 10
0
votes
3
replies
1.6k
views
using packages with conda
snakemake conda scinkd
updated 17 days ago by 89k • written 17 days ago by • 0
1
vote
2
replies
1.1k
views
limmaFit error when comparing TCGA RNA-Seq data
R TCGA LIMMA
16 days ago by vernonlim98 • 0
0
votes
1
reply
1.1k
views
X chromosome male and female imputation
chrX GWAS imputation
updated 17 days ago by ★ 2.5k • written 18 days ago by ▴ 10
3
votes
1
reply
1.5k
views
conda create PackagesNotFoundError
conda
updated 18 days ago by ★ 1.2k • written 18 days ago by • 0
1
vote
0
replies
1.0k
views
Job: Hiring FT Remote Nextflow engineer to build ML workflows for cancer genomics
nextflow jobs hiring engineer
18 days ago by L ▴ 10
0
votes
1
reply
1.3k
views
Genome Contamination Check with Blobtools
diamond blobtools genome blast
updated 18 days ago by 154k • written 18 days ago by ▴ 30
3
votes
6
replies
6.0k
views
Orthofinder Not Mapping to Any Orthogroups
orthology orthoDB BLAST orthofinder
18 days ago by saamhasan55 ▴ 30
2
votes
2
replies
1.7k
views
LASSO parameter selection: lambda min vs lambda 1se
LASSO
18 days ago by nuorain ▴ 40
0
votes
0
replies
1.1k
views
News: Online course: Introduction to Nanopore Direct RNA Sequencing (RNA004)
RNA004 DirectRNAseq Nanopore RNAModifications
18 days ago by Physalia-courses ★ 2.7k
0
votes
2
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2.2k
views
Feasibility of detecting PCR-chimeric reads with Machine Learing (ML) for organelle genome assemblies
ML assembly chimeric mitochondria
updated 18 days ago by 3.9k • written 19 days ago by • 0
2
votes
2
replies
2.3k
views
Help understanding this per base sequence content failure fastqc plot
fastqc
updated 18 days ago by 16k • written 19 days ago by ▴ 900
17
votes
5
replies
4.3k
views
Linear regression vs DESeq2 models for DEG analysis
Bulk seq analysis RNA
updated 19 days ago by 89k • written 20 days ago by • 0
1
vote
2
replies
2.9k
views
how to explain the sample size discrepancy in UCSC Xena
UCSC Xena
19 days ago by nuorain ▴ 40
0
votes
2
replies
2.1k
views
DNA copy number blacklist for excluding common unreliable regions
blacklist copy number
16 days ago by yura.grabovska ▴ 850
0
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3
replies
2.8k
views
Functional prediction for proteins of bacteria.
predection Proteins Fuctional bacteria
updated 15 days ago by 8.0k • written 21 days ago by ▴ 30
2
votes
3
replies
5.9k
views
What happened to biomart.org
biomart
updated 21 days ago by 23k • written 22 days ago by ▴ 10
0
votes
4
replies
5.9k
views
real time PCR data analysis
PCR donor effect
updated 20 days ago by 89k • written 22 days ago by ▴ 50
8
votes
4
replies
6.3k
views
Forum: Looking to learn practical bioinformatics
learn practical collaborate
22 days ago by Upesh ▴ 20
0
votes
0
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3.2k
views
News: Workshop: Virtual ChIP-Seq / ATAC-Seq – Oct. 28–30, 2025
workshop ATACSeq ChIPSeq virtual UConn
22 days ago by zsc25001 ▴ 10
4
votes
5
replies
6.4k
views
Does this adapter content from fastqc to warrant trimming prior to alignment?
fastqc bwa-mem multiqc
17 days ago by curious ▴ 900
3
votes
5
replies
5.2k
views
Restricting ncbi-genome-download (bacteria, viral, fungi, archaea, protozoa) to a specif host
ncbi
updated 22 days ago by 154k • written 22 days ago by ▴ 10
3
votes
12
replies
6.2k
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
updated 22 days ago by • 0 • written 18 months ago by ▴ 40
3
votes
2
replies
4.5k
views
How to overcome OS return value: 4 with SPAdes
Spades de novo genome assemble
23 days ago by marongiu.luigi ▴ 770
2
votes
2
replies
4.5k
views
Understanding the relationship between hhr and a3m output of HHblits
hhblits hhsuite
updated 23 days ago by 22k • written 23 days ago by ▴ 10
0
votes
1
reply
4.7k
views
TOPMed Imputation - More than 10000 allele switches
imputation topmed
updated 23 days ago by • 0 • written 10 weeks ago by • 0
0
votes
4
replies
5.4k
views
Help with Model
model modelling
updated 23 days ago by 22k • written 24 days ago by • 0
1
vote
2
replies
4.7k
views
Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
16s v3-v4 qiime2 kraken2 bracken
23 days ago by Christopher ▴ 10
1
vote
3
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5.2k
views
SNP calling with bacterial assembled genome
variant-calling SNP bacteria
updated 23 days ago by 154k • written 24 days ago by • 0
0
votes
2
replies
5.2k
views
Help with species tree with orthofinder, iqtree and branch labeling
iqtree trimal CAFE5 orthofinder mafft
updated 24 days ago by 154k • written 25 days ago by ▴ 190
0
votes
0
replies
4.4k
views
BWA alt-aware pipeline troubleshooting
alt-aware BWA samtools
24 days ago by Duy • 0
0
votes
0
replies
4.3k
views
News: Last 3 seats: In-Person Single-Cell RNA-Seq Data Analysis Workshop (October 6-8 in Berlin)
scRNAseq singleCell transcriptomics
24 days ago by ecSeq Bioinformatics ▴ 20
2
votes
5
replies
6.2k
views
cellranger mkref fail/error
mkref multiple_species customtranscriptome cellranger transcriptome
updated 19 days ago by 3.4k • written 24 days ago by • 0
0
votes
2
replies
5.5k
views
Methods to analyse structural similarity: co-evolution vs convergence
genomics comparative proteomics evolutionary
updated 24 days ago by 22k • written 25 days ago by • 0
3
votes
1
reply
4.7k
views
vcf multisample
multi-sample genomic vcf
updated 24 days ago by 166k • written 25 days ago by • 0
6
votes
9
replies
7.7k
views
Genome Assembly QC from BAM files
QC assembly BAM HiFi
updated 23 days ago by 154k • written 25 days ago by ▴ 250
0
votes
0
replies
4.7k
views
News: Last 2 Seats – Genome Assembly with Oxford Nanopore (29 Sept–3 Oct)
GenomeAssembly Nanopore longreads
25 days ago by Physalia-courses ★ 2.7k
8
votes
9
replies
20k
views
8 follow
WGCNA package in R: dendogram plot error
wgcna R
updated 26 days ago by • 0 • written 8.7 years ago by ▴ 40
7
votes
3
replies
9.3k
views
Different UMAP for batch correction in R and Pytho
harmony UMAP
25 days ago by Madiha ▴ 20
0
votes
1
reply
6.9k
views
How to properly assemble phage genomes?
metagenomics assembly genome virus phage
updated 26 days ago by 22k • written 28 days ago by ▴ 770
0
votes
4
replies
6.4k
views
Forum: Developing a genomics ML model using bytes?
Learning Machine Genomics Bytes
updated 25 days ago by 15k • written 26 days ago by ▴ 10
1
vote
13
replies
8.0k
views
miRNA low mapping ratings
mirna bowtie1 preprocessing counts aligment
23 days ago by Ant ▴ 50
0
votes
4
replies
6.8k
views
Trouble when installing arb
arb
updated 26 days ago by 154k • written 2.9 years ago by ▴ 30
1
vote
0
replies
5.6k
views
News: Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
transcriptomics RNAseq
27 days ago by soledad.esteban ▴ 10
0
votes
0
replies
6.1k
views
rsid in full data table for GSA array but not in the final vcf file
array GSA
28 days ago by 1769mkc ★ 1.3k
122,039 results • Page 3 of 2441
Recent Votes
Answer: High Variability when Peak Calling with SEACR
A: Get chromosome sizes from fasta file
How to keep the top hits only in the output file of hmmscan?
A: How to keep the top hits only in the output file of hmmscan?
ProbeID to Gene Symbol Mapping in Microarray data analysis using R
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
Answer: Choosing enrichment analysis tool
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Comment: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates by Thanujay S • 0
Hey! Yes, in the pilot version of the script, conversions were supported only for Homo sapiens. With the release of version 0.2 (today), su…
Answer: DE analysis in nascent RNA Seq based on intron sequences by dsull ★ 7.7k
Yes, that’s fine; I don’t see why nascent transcripts should be treated differently than mature transcripts in DE analysis.
Comment: High Variability when Peak Calling with SEACR by RD ▴ 30
Hi Jared, I’m trying to figure out the right parameters to use with MACS3 for CUT&RUN data. My understanding is that it’s best to convert t…
Answer: SNP calling ONT sequenced files by Момчил ▴ 10
Yes, one can say that ONT reads do still have higher error rates in comparison to Illumina short reads, but the situation has improved sign…
Comment: MOuse Testis Enhancer region by GenoMax 154k
That web site is off-line for everyone. You will have to look for an alternate option.
Answer: Is there a way to produce/convert nhmmer output to a bed file? by colindaven 8.0k
To make it a bit clearer for nhmmer specifically, I used the following. This is code used in nextflow. # run nhmmer nhmm…
Comment: reference-guided assembly tools for short read data? by lieven.sterck 16k
there are several options to choose from, doing a quick google search will give you a lot. The main thing to keep in mind is to choose one …
Comment: Python deconvolution tools for bulk RNA-seq data by Arup Ghosh 3.4k
Check the [Bulk2Single][1] option from [OmicVerse][2] framework. [1]: https://omicverse.readthedocs.io/en/latest/Tutorials-bulk2single/…
Comment: reference-guided assembly tools for short read data? by michael.ante ★ 4.0k
I don't know how well it works for plants, but I worked with [Saute][1] and it was doing well for reference based assemblies. [1]: http…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by ATpoint 89k
Most likely a download artifact. First I would re-download and inly if that fails again then do repairing. ftp is primitive, it's just hit …
Answer: Python deconvolution tools for bulk RNA-seq data by ATpoint 89k
Imo you are approaching this the wrong way. R packages for deconvolution that are heqavily used and cited do exist, for example MuSiC and B…
Comment: MOuse Testis Enhancer region by Bioinformatics_16 • 0
@genomax Do you have access to this list? If so, could you please share it? I need it urgently.
Comment: HDOCK Server Error! by Jannatul Ferdous • 0
Tried that but unfortunately, the problem still persists :( Thanks for your response though!
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq by LChart 5.1k
While Himar1 inserts in TA motifs, the library is generated following restriction enzyme treatment (Mmrl) and ligation. The Mmrl sequence i…
Comment: Is it possible to do standard GSEA in R? by mbramble • 0
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
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