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mirdeep2 help
mirdeep2 virus
updated 2.5 years ago by 6.2k • written 2.5 years ago by • 0
2
votes
5
replies
1.2k
views
How to check a gene in an open chromatin region or not?
ATAC-seq
2.4 years ago by Chris ▴ 360
0
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0
replies
679
views
Issues with PhyloCSF installation through opam and docker
phylocsf opam docker
2.5 years ago by Daniel ▴ 40
0
votes
0
replies
893
views
Do I need to do QC before demultiplexing hashtags with hashsolo?
scanpy hashtag hashsolo RNAseq
2.5 years ago by bioinfo ▴ 160
1
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1
reply
2.0k
views
Issues installing PhyloCSF for VEP: opam install ocamlbuild
PhyloCSF VEP ensembl
updated 2.5 years ago by ▴ 40 • written 5.6 years ago by ▴ 120
0
votes
1
reply
3.7k
views
gunzip error: trailing garbage ignored
vcf gzip gz plink
updated 2.5 years ago by ★ 30k • written 2.5 years ago by • 0
0
votes
3
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3.6k
views
Error while running nf-core/rnaseq pipeline
nf-core
updated 2.5 years ago by ▴ 410 • written 2.5 years ago by • 0
0
votes
7
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2.0k
views
How to test DEGs from microarray data on RNA-seq dataset
microarray differential limma RNA-seq expression prediction
2.4 years ago by Llander • 0
0
votes
0
replies
645
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
R Network-Analysis Bioconductor Systems-Biology
updated 2.4 years ago by 45k • written 2.5 years ago by ★ 2.6k
0
votes
2
replies
902
views
single cell RNA analysis
Single RNA cell Transciptomics
2.5 years ago by archanaverma433 ▴ 10
2
votes
4
replies
2.5k
views
tx2gene.txt : transcript-to-gene mapping file
tx2gene mapping
updated 2.5 years ago by 103k • written 2.5 years ago by ▴ 10
0
votes
0
replies
530
views
Can I use psiiblast profile as query?
protein blast
2.5 years ago by Xylanaser ▴ 80
0
votes
2
replies
1.1k
views
How to map genomic sequence to protein functions or domains?
GRange Genome Ensembldb annotation
updated 2.5 years ago by 8.0k • written 2.5 years ago by ▴ 140
0
votes
1
reply
848
views
Liger find a sub cluster under one cluster
liger
2.4 years ago by Andy ▴ 120
0
votes
0
replies
646
views
rtracklayer import.chain not accpect chain file
R rtracklayer liftOver
2.5 years ago by octpus616 ▴ 120
0
votes
2
replies
1.1k
views
Is there a SILVA database version with only prokaryotes?
taxonomy SILVA 16S
2.5 years ago by SushiRoll ▴ 140
0
votes
0
replies
682
views
News: Course - Phylogenetic Comparative Methods in R
Comparative-Methods R Phylogenetics
updated 2.4 years ago by 45k • written 2.5 years ago by ★ 2.6k
1
vote
4
replies
1.1k
views
Merge the same gene and get percentage of gene from the output file of mosdepth tool
mosdepth
2.5 years ago by anii • 0
4
votes
6
replies
6.4k
views
ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue
ChIP-Seq MACS2
updated 2.5 years ago by • 0 • written 6.8 years ago by 6.5k
0
votes
0
replies
650
views
Functional differences in bacterial genomes within a genus
genome bacteria pathway function
2.5 years ago by lstn • 0
1
vote
0
replies
551
views
Analysis of unknown lncRNAs
lncRNA differential RNA-seq target-identification expression
updated 2.5 years ago by 2.9k • written 2.5 years ago by ▴ 20
1
vote
2
replies
1.7k
views
stacks ref_map.pl ERROR 128
ref_map stacks filtering BAM VCF
2.5 years ago by Ale • 0
1
vote
2
replies
1.1k
views
How to split a fastq file to multiples fastq files
fastq sequencing rna-seq
2.5 years ago by Apex92 ▴ 320
0
votes
0
replies
493
views
Species tree size limits for CAFE5
CAFE family phylogeny tree species gene
2.5 years ago by Bo • 0
0
votes
1
reply
1.0k
views
vcf.Reader() in Python doesn't read my VCF
vcf python wxpython
updated 2.5 years ago by 6.2k • written 2.5 years ago by • 0
0
votes
0
replies
528
views
Per sequence GC content graph showing two peaks in ChIPseq data analysis
FastQC content ChIPseq Per GC sequence
2.5 years ago by shashianand15 • 0
0
votes
0
replies
391
views
Per base sequence content warning in ChIPseq data FastQC analysis
ChIP-seq FastQC
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
0
votes
0
replies
518
views
Creating phylogenetic tree in newick format from a given list of Scientific names.
newick creating Phylogenetic tree format
2.5 years ago by nivedita.home • 0
1
vote
5
replies
1.5k
views
Modify fasta file header
fastfile modification
updated 2.5 years ago by 13k • written 2.5 years ago by • 0
1
vote
9
replies
3.7k
views
kallisto bootstrap / condo installation problem
hfd5 kallisto condo
updated 2.5 years ago by ★ 7.7k • written 2.5 years ago by ▴ 10
3
votes
4
replies
2.2k
views
Scan multiple sequences on multiple hmm profiles
Hmm hmmer
updated 2.5 years ago by ★ 30k • written 2.5 years ago by ▴ 150
1
vote
2
replies
3.5k
views
Maintaining the coverage filter in mmseqs for cascaded clustering
coverage searches mmseqs clustering sequence
2.5 years ago by Victor • 0
0
votes
0
replies
578
views
Performing GO analysis from Differential Peaks
clusterProfiler Signac analysis atac-seq go
2.5 years ago by bioinformatics.girl ▴ 30
0
votes
0
replies
812
views
How to save the digital percentage of `ChIPseeker::plotAnnoPie()` to a table?
ChIPseeker
2.5 years ago by Dan ▴ 180
7
votes
3
replies
3.0k
views
Different results between clusterProfiler and Enrichr
enrichr clusterProfiler
2.4 years ago by abbas89 ▴ 30
0
votes
2
replies
1.6k
views
Compare SMILES from PDBQT file and SDF File
Docking Molecular
2.5 years ago by bioinformatics.queries ▴ 70
3
votes
2
replies
1.2k
views
Does ROSE include traditional enhancer in the analysis output?
ROSE Super enhancers
2.5 years ago by b8921019 • 0
0
votes
1
reply
1.4k
views
Michigan Imputation server failed job
michigan-imputation-server vcf
2.5 years ago by Najla • 0
2
votes
4
replies
1.6k
views
Having problem on doing edgeR anlysis- cant create the DGE list through readbismark2DGE function.
EDGER R
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
3
votes
2
replies
1.7k
views
How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e …
metagenomics blast spades megahit assembly
updated 2.5 years ago by ★ 30k • written 2.5 years ago by ▴ 20
0
votes
0
replies
532
views
BIONIC network integration package
network expression regulatory python gene
2.5 years ago by sweta.roycarson • 0
0
votes
1
reply
852
views
DESEQ2 FORMULAS FOR PAIRED SAMPLES
samples deseq2 design paired
updated 2.5 years ago by 22k • written 2.5 years ago by • 0
0
votes
2
replies
2.1k
views
News: 20% Off - Next-Generation Sequencing Data Analysis: A Practical Introduction (May 3-5, 2023 in Munich, Germany)
NGS DNA-Seq variant-calling RNA-Seq workshop
2.5 years ago by David Langenberger 11k
0
votes
1
reply
735
views
Please help with edgeR script
edgeR
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 30
0
votes
0
replies
639
views
Inferring relative gene abundance from short reads
metagenomics read 16S short mapping
2.5 years ago by SushiRoll ▴ 140
0
votes
3
replies
1.5k
views
How to combine multiple PWMs to identify most likely binding motif
combine PWM CLIP-seq RBP TF
updated 2.5 years ago by ★ 4.0k • written 2.5 years ago by • 0
2
votes
1
reply
1.4k
views
Estimating Nucleotide diversity (Pi) from VCF file in polyploid organism (tetraploid)
vcf genetics population polypoid
updated 2.5 years ago by ★ 3.1k • written 2.5 years ago by 56k
0
votes
1
reply
1.3k
views
SoupX with scDblFinder, matrix error
r scdblfinder seurat soupx
updated 2.5 years ago by 89k • written 2.5 years ago by • 0
1
vote
2
replies
816
views
design formula DEG paired design
R
2.5 years ago by Caro ▴ 10
0
votes
0
replies
470
views
Blog: We want to speak to Precision Oncology researches
cancer TCGA mutations genomics startup
updated 2.5 years ago by 166k • written 2.5 years ago by • 0
121,999 results • Page 266 of 2440
Recent Votes
Comment: Differences between published differential gene expression results and own analy
A: Fold change - a final explanation
Answer: Doubt on docking
Answer: SNP calling ONT sequenced files
Answer: SNP calling ONT sequenced files
Answer: Combine a directory of GVCF files with gatk CombineGVCFs
Answer: Combine a directory of GVCF files with gatk CombineGVCFs
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Recent Replies
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
I think `1ubq_Repair_1.pdb` is an intermediate file, and the other 3 files matter. But I use FoldX rarely, so you will have to verify this …
Comment: Difficulty running FoldX in linux by strayeroliver • 0
That's great, @mensur. Thank you. I have a run that operates on 1ubq_Repair.pdb and produces a 'Dif_1ubq_Repair.fxout' now, even with numbe…
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Billy Rowell ▴ 510
Is there a reason you'd like to use IPA over, for instance, hifiasm? I'd recommend starting with hifiasm. For pbipa, try downgrading to s…
Answer: Active site using castpfold by dthorbur ★ 3.1k
This is very similar to your recent [post](https://www.biostars.org/p/9615406/) - if you aren't going to provide the protein example for a …
Answer: Differences between published differential gene expression results and own analy by Zhenyu Zhang ★ 1.3k
1. When you said "the same dataset", are you sure about the files are the same, or you just mean the same list of patients? There are many …
Answer: downloading raw bam files from pacbio sequencer by Arup Ghosh 3.4k
Try: https://www.google.com/search?q=site:https://downloads.pacbcloud.com/public/dataset/+%22subreads%22
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
If they are not available at PacBio site then your chances of getting them are going to be significantly reduced. Only other source may be …
Comment: downloading raw bam files from pacbio sequencer by pranavdatar01 • 0
Yes, I did check. They don't have any.
Comment: downloading raw bam files from pacbio sequencer by pranavdatar01 • 0
I want to download the HDF5 .bax.h5 files or BAM/SAM .subreads.[bs]am files which out from the pacbio sequencer. Are there any sample demo …
Comment: installation of package ‘DESeq2’ had non-zero exit status by GenoMax 154k
> Installation paths not writeable, unable to update packages Are you a normal user on a system administered by other admins?
Comment: installation of package ‘DESeq2’ had non-zero exit status by lieven.sterck 16k
Hi https://www.biostars.org/u/151679/ welcome to the forum. Quite an extensive post but I can't seem to find a real question? Please don…
Comment: Pseudogene - scarce info by mf810 • 0
That's actually a huge help, thank you so much! Even if the finding is there's no relevant findings, it's nice to have someone else check…
Answer: Transverse data by basu • 0
Sounds like you’ve got a data party going on—too many duplicates crashing it! If you need a quick fix for those pesky repeats, maybe check …
Answer: Pseudogene - scarce info by Mensur Dlakic ★ 30k
> The gene plays a pivotal role in some pathways of the immune response, but tbh I could'nt find any mention of my pseudogene on the linked…
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
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