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Python deconvolution tools for bulk RNA-seq data
RNA-seq bulk-rna-seq Deconvolution python transcriptomics
8 hours ago by AlexStar ▴ 200
1
vote
1
reply
93
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 10 hours ago by 154k • written 14 hours ago by • 0
2
votes
5
replies
171
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BWA-MEM with an array of files
alignment array BWA-MEM
updated 12 hours ago by 5.1k • written 14 hours ago by ▴ 50
847
votes
170
replies
215k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook training
updated 15 days ago by 3.6k • written 8.9 years ago by 103k
1
vote
4
replies
148
views
reference-guided assembly tools for short read data?
genomics assembly bioinformatics
13 hours ago by Hani • 0
0
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0
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63
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interpretation of the results obtained with digital PCR
dPCR
16 hours ago by Lorenzo • 0
1
vote
3
replies
140
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MOuse Testis Enhancer region
enhancer
1 hour ago by Bioinformatics_16 • 0
0
votes
0
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94
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Job: Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics glycoproteomics proteomics machine-learning omics
10 hours ago by Daniel • 0
2
votes
1
reply
162
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Modeling/simulations using SNPs data
SNP
updated 1 day ago by ★ 2.2k • written 1 day ago by • 0
2
votes
1
reply
158
views
Strugling on the 3'rule of HGVS
notation hgvs variants
updated 1 day ago by 23k • written 1 day ago by ▴ 120
13
votes
17
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4.8k
views
Extract fastq sequences based on date/time (which is in the header)
sequence fastq
updated 1 day ago by ▴ 20 • written 7.1 years ago by ▴ 10
2
votes
5
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3.0k
views
Filter nanopore fastq files by start time
nanopore fastq filter start time
updated 1 day ago by ▴ 20 • written 6.3 years ago by ▴ 10
1
vote
3
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316
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Choosing enrichment analysis tool
DAVID Metascape Enrichr
updated 1 day ago by 22k • written 3 days ago by • 0
3
votes
4
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198
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Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit q-score fastqc 16s-wf nanoplot
1 day ago by k-tarasov ▴ 10
4
votes
4
replies
564
views
How to create a consensus of a contig with samtools or bbmap?
contig bbmap consensus samtools genome
updated 1 day ago by ★ 1.3k • written 12 days ago by ▴ 770
1
vote
1
reply
182
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq scRNA-seq snRNA-seq
updated 1 day ago by 89k • written 2 days ago by • 0
0
votes
1
reply
130
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Configuration file for DSP WTA
DSP
updated 1 day ago by 154k • written 1 day ago by ▴ 10
0
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0
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94
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News: 1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics RNA-Seq Expression Differential
1 day ago by ecSeq Bioinformatics ▴ 20
0
votes
2
replies
219
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What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
2 days ago by fra.r.silvestro ▴ 10
0
votes
0
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130
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Does the weights file stay the same for a different model organism
machine learning weights bioinformatics
updated 2 days ago by 154k • written 2 days ago by • 0
0
votes
2
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183
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HDOCK Server Error!
HDOCK Docking
1 hour ago by Jannatul Ferdous • 0
3
votes
1
reply
177
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Variant Normalization
vcf
updated 2 days ago by 103k • written 2 days ago by • 0
1
vote
2
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547
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Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq DEA TCGA Learning Machine
2 days ago by yordany.perdigon • 0
0
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0
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139
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News: Autumn School in Bioinformatics – Online, 20–24 October
NGS Phylogenomics RNAseq Singularity Docker
updated 2 days ago by 166k • written 2 days ago by ★ 2.7k
0
votes
1
reply
183
views
Issue with Snippy 4.6.0
Snippy Core.vcf SNP
updated 2 days ago by 154k • written 2 days ago by • 0
0
votes
2
replies
231
views
Cells from normal sample were incorrectly classified as tumor cells using copykat
copykat scRNA-seq cell tumor
21 hours ago by tujuchuanli ▴ 130
0
votes
1
reply
185
views
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
mitochondria Assembly Genome Novoplasty
updated 2 days ago by 154k • written 2 days ago by • 0
3
votes
1
reply
255
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 3 days ago by 89k • written 3 days ago by ▴ 50
20
votes
13
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1.3k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell software commercial gui
3 days ago by firestar ★ 1.7k
1
vote
0
replies
204
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Tool: ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf rna-seq assembly annotation transcriptome
4 days ago by Ales ▴ 90
0
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10
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678
views
Tool: Brave: Bioinformatics Reactive Analysis and Visualization Engine
Docker R Nextflow Python React
1 day ago by Edward • 0
0
votes
2
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491
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scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony scVI single cell
updated 4 days ago by 89k • written 9 days ago by ▴ 110
1
vote
0
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231
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News: Manual Genome Curation using PretextView course
Genome-Assembly PretextView HI-C Manuel-Curation
5 days ago by Physalia-courses ★ 2.7k
4
votes
11
replies
872
views
DESeq2 on metagenome KO counts
abundance KEGG KO deseq metagenome gene
updated 5 days ago by ▴ 190 • written 6 days ago by ▴ 240
0
votes
0
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272
views
News: Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial Proteomics omics
updated 6 days ago by 154k • written 6 days ago by ▴ 110
2
votes
1
reply
320
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell rna-detection FACS doublet scRNA-seq
updated 3 days ago by 45k • written 6 days ago by ▴ 50
1
vote
1
reply
385
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools combine VCF
updated 5 days ago by ★ 4.3k • written 6 days ago by ▴ 130
4
votes
4
replies
446
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker uniprot proteomics annotation trembl
updated 6 days ago by ★ 2.4k • written 7 days ago by • 0
7
votes
2
replies
374
views
Recommendations for 200 SNP markers genotyping
sequencing DNA genotyping marker
updated 6 days ago by ▴ 190 • written 6 days ago by ▴ 10
0
votes
3
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472
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Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run genomic features
updated 5 days ago by ★ 1.7k • written 8 days ago by ▴ 40
0
votes
3
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433
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end fastq paired
updated 3 days ago by 16k • written 6 days ago by ▴ 130
1
vote
2
replies
371
views
Reasonable number of SNPs in a bacterial genome.
SNP bacteria
updated 3 days ago by ★ 4.0k • written 7 days ago by • 0
2
votes
6
replies
756
views
Difficulty running FoldX in linux
DDG foldx
updated 7 days ago by • 0 • written 9 days ago by ▴ 10
0
votes
2
replies
397
views
Active site using castpfold
activesite castpfold Docking
updated 7 days ago by ★ 30k • written 7 days ago by • 0
5
votes
12
replies
1.3k
views
6 follow
Differences between published differential gene expression results and own analysis on RNA-seq data
R TCGA LIMMA
updated 7 days ago by ★ 1.3k • written 14 days ago by • 0
1
vote
4
replies
531
views
Problems with PacBio's Improved Phased Assembler (IPA)
pacbio hifi assembly genome
6 days ago by Panos ★ 1.8k
0
votes
6
replies
587
views
downloading raw bam files from pacbio sequencer
raw bam_file raw_subreads reads
updated 7 days ago by 154k • written 8 days ago by • 0
0
votes
0
replies
274
views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
PLM mapping LLM extraction Relation
7 days ago by DEPANSHI • 0
1
vote
2
replies
613
views
installation of package ‘DESeq2’ had non-zero exit status
Bioinformatics
updated 7 days ago by 154k • written 7 days ago by • 0
0
votes
1
reply
326
views
Checkm results differ from database info
Checkm
updated 3 days ago by 45k • written 7 days ago by • 0
122,034 results • Page 1 of 2441
Recent Votes
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
Answer: Choosing enrichment analysis tool
Answer: reference-guided assembly tools for short read data?
Answer: BWA-MEM with an array of files
Comment: BWA-MEM with an array of files
Answer: MOuse Testis Enhancer region
Dependent samples in DESeq2 - How to incorporate random factor?
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Recent Replies
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.
Comment: BWA-MEM with an array of files by LChart 5.1k
For solution 1, because bwa streams the data, you can save some space by using a named pipe: ```bash mkfifo Sample_23/concat.R1.fq.gz find…
Comment: reference-guided assembly tools for short read data? by Hani • 0
Either de novo or reference based genome assembly using Illumina PE short reads
Comment: reference-guided assembly tools for short read data? by lieven.sterck 16k
which purpose specifically?
Comment: reference-guided assembly tools for short read data? by Hani • 0
In regards to your comment about synteny analysis, I suspected that would be the case. In regards to tools for these purposes, do you perso…
Comment: BWA-MEM with an array of files by lieven.sterck 16k
aha, but bwa mem only takes at best 1 pair of fastq files as input, not a whole list. So to achieve this efficiently do what https://www.b…
Answer: reference-guided assembly tools for short read data? by lieven.sterck 16k
Not silly at all and done before many times. So yes that is a valid approach. There are certainly a number of tools around that can do this…
Comment: BWA-MEM with an array of files by garcesj ▴ 50
None in particular (that's why I didn't indicate it). It just gives back the BWA-MEM help.
Answer: BWA-MEM with an array of files by Pierre Lindenbaum 166k
solution 1: merge each R1 and R2 files into one. Beware, the order of the fastq files must be the same find Sample_23 -type f -name …
Comment: BWA-MEM with an array of files by lieven.sterck 16k
what is the (error) message you get, if any?
Comment: MOuse Testis Enhancer region by Bioinformatics_16 • 0
![enter image description here][1] [1]: /media/images/0241beed-c410-47b0-b8e2-43534232
Answer: MOuse Testis Enhancer region by GenoMax 154k
It is not just you the site appears to be down right now: https://downforeveryoneorjustme.com/enhanceratlas.org?proto=http&www=1
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