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122,039 results • Page 1 of 2441
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0
replies
23
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Homology Directed Repair in Crispr-Cas9 gene editing/deletion
crispr editing cas9 gene
1 hour ago by hiname • 0
0
votes
0
replies
47
views
Reference VCF with "chr" contigs instead of "number"
file reference VCF
6 hours ago by GPR ▴ 390
0
votes
1
reply
104
views
DE analysis in nascent RNA Seq based on intron sequences
Normalization DESeq2 RNA-Seq Nascent
updated 9 hours ago by ★ 7.7k • written 14 hours ago by ▴ 80
847
votes
170
replies
216k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook training
updated 16 days ago by 3.6k • written 8.9 years ago by 103k
4
votes
4
replies
591
views
SNP calling ONT sequenced files
ONT SNPs
updated 16 hours ago by ▴ 10 • written 9 days ago by ▴ 280
0
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0
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67
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News: RAD-seq Data Analysis - online course
Phylogenomics RADseq Genomics Population Stacks
20 hours ago by Physalia-courses ★ 2.7k
0
votes
0
replies
75
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Error "no rows to aggregate" using makeFunctionalPrediction() Tax4fun2
R Tax4fun2 prediction functional makeFunctionalPrediction
23 hours ago by Marine • 0
7
votes
8
replies
2.4k
views
Is there a way to produce/convert nhmmer output to a bed file?
bed nhmmer
updated 1 day ago by 8.0k • written 5.0 years ago by ▴ 90
0
votes
2
replies
194
views
Python deconvolution tools for bulk RNA-seq data
RNA-seq bulk-rna-seq Deconvolution python transcriptomics
updated 1 day ago by 3.4k • written 1 day ago by ▴ 200
1
vote
1
reply
146
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 1 day ago by 154k • written 1 day ago by • 0
2
votes
5
replies
251
views
BWA-MEM with an array of files
alignment array BWA-MEM
updated 1 day ago by 5.1k • written 1 day ago by ▴ 50
1
vote
6
replies
271
views
reference-guided assembly tools for short read data?
genomics assembly bioinformatics
updated 1 day ago by 16k • written 1 day ago by • 0
0
votes
0
replies
108
views
interpretation of the results obtained with digital PCR
dPCR
1 day ago by Lorenzo • 0
1
vote
4
replies
250
views
MOuse Testis Enhancer region
enhancer
updated 23 hours ago by 154k • written 2 days ago by • 0
0
votes
0
replies
145
views
Job: Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics glycoproteomics proteomics machine-learning omics
1 day ago by Daniel • 0
2
votes
1
reply
207
views
Modeling/simulations using SNPs data
SNP
updated 2 days ago by ★ 2.2k • written 2 days ago by • 0
2
votes
1
reply
203
views
Strugling on the 3'rule of HGVS
notation hgvs variants
updated 2 days ago by 23k • written 3 days ago by ▴ 120
13
votes
17
replies
4.9k
views
Extract fastq sequences based on date/time (which is in the header)
sequence fastq
updated 2 days ago by ▴ 20 • written 7.1 years ago by ▴ 10
2
votes
5
replies
3.0k
views
Filter nanopore fastq files by start time
nanopore fastq filter start time
updated 2 days ago by ▴ 20 • written 6.3 years ago by ▴ 10
1
vote
3
replies
367
views
Choosing enrichment analysis tool
DAVID Metascape Enrichr
updated 2 days ago by 22k • written 4 days ago by • 0
3
votes
4
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257
views
Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit q-score fastqc 16s-wf nanoplot
2 days ago by k-tarasov ▴ 10
4
votes
4
replies
608
views
How to create a consensus of a contig with samtools or bbmap?
contig bbmap consensus samtools genome
updated 3 days ago by ★ 1.3k • written 14 days ago by ▴ 770
1
vote
1
reply
230
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq scRNA-seq snRNA-seq
updated 3 days ago by 89k • written 3 days ago by • 0
0
votes
1
reply
176
views
Configuration file for DSP WTA
DSP
updated 2 days ago by 154k • written 3 days ago by ▴ 10
0
votes
0
replies
136
views
News: 1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics RNA-Seq Expression Differential
3 days ago by ecSeq Bioinformatics ▴ 20
0
votes
2
replies
273
views
What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
3 days ago by fra.r.silvestro ▴ 10
0
votes
0
replies
177
views
Does the weights file stay the same for a different model organism
machine learning weights bioinformatics
updated 3 days ago by 154k • written 3 days ago by • 0
0
votes
2
replies
268
views
HDOCK Server Error!
HDOCK Docking
1 day ago by Jannatul Ferdous • 0
3
votes
1
reply
218
views
Variant Normalization
vcf
updated 3 days ago by 103k • written 3 days ago by • 0
1
vote
2
replies
643
views
Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq DEA TCGA Learning Machine
3 days ago by yordany.perdigon • 0
0
votes
0
replies
177
views
News: Autumn School in Bioinformatics – Online, 20–24 October
NGS Phylogenomics RNAseq Singularity Docker
updated 4 days ago by 166k • written 4 days ago by ★ 2.7k
0
votes
1
reply
224
views
Issue with Snippy 4.6.0
Snippy Core.vcf SNP
updated 4 days ago by 154k • written 4 days ago by • 0
0
votes
2
replies
282
views
Cells from normal sample were incorrectly classified as tumor cells using copykat
copykat scRNA-seq cell tumor
2 days ago by tujuchuanli ▴ 130
0
votes
1
reply
225
views
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
mitochondria Assembly Genome Novoplasty
updated 3 days ago by 154k • written 4 days ago by • 0
3
votes
1
reply
293
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 4 days ago by 89k • written 5 days ago by ▴ 50
20
votes
13
replies
1.3k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell software commercial gui
5 days ago by firestar ★ 1.7k
1
vote
0
replies
241
views
Tool: ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf rna-seq assembly annotation transcriptome
5 days ago by Ales ▴ 90
0
votes
10
replies
751
views
Tool: Brave: Bioinformatics Reactive Analysis and Visualization Engine
Docker R Nextflow Python React
2 days ago by Edward • 0
0
votes
2
replies
528
views
scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony scVI single cell
updated 6 days ago by 89k • written 10 days ago by ▴ 110
1
vote
0
replies
266
views
News: Manual Genome Curation using PretextView course
Genome-Assembly PretextView HI-C Manuel-Curation
7 days ago by Physalia-courses ★ 2.7k
4
votes
11
replies
937
views
DESeq2 on metagenome KO counts
abundance KEGG KO deseq metagenome gene
updated 6 days ago by ▴ 190 • written 8 days ago by ▴ 240
0
votes
0
replies
305
views
News: Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial Proteomics omics
updated 7 days ago by 154k • written 7 days ago by ▴ 110
2
votes
1
reply
359
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell rna-detection FACS doublet scRNA-seq
updated 4 days ago by 45k • written 8 days ago by ▴ 50
1
vote
1
reply
426
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools combine VCF
updated 6 days ago by ★ 4.3k • written 8 days ago by ▴ 130
4
votes
4
replies
495
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker uniprot proteomics annotation trembl
updated 8 days ago by ★ 2.4k • written 8 days ago by • 0
7
votes
2
replies
411
views
Recommendations for 200 SNP markers genotyping
sequencing DNA genotyping marker
updated 8 days ago by ▴ 190 • written 8 days ago by ▴ 10
0
votes
3
replies
519
views
Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run genomic features
updated 6 days ago by ★ 1.7k • written 10 days ago by ▴ 40
0
votes
4
replies
524
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end fastq paired
updated 1 day ago by 89k • written 8 days ago by ▴ 130
1
vote
2
replies
411
views
Reasonable number of SNPs in a bacterial genome.
SNP bacteria
updated 5 days ago by ★ 4.0k • written 8 days ago by • 0
2
votes
6
replies
822
views
Difficulty running FoldX in linux
DDG foldx
updated 8 days ago by • 0 • written 10 days ago by ▴ 10
122,039 results • Page 1 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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Recent Replies
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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