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121,332 results • Page
1 of 2427
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0
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5
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Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
5 minutes ago by
KABILAN
▴ 130
0
votes
0
replies
10
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
10 minutes ago by
rbpdee
▴ 50
0
votes
3
replies
107
views
How to deal with intermediate files
procedures
data
operations
updated 10 minutes ago by
GenoMax
151k • written 13 hours ago by
ramiro.barrantes
▴ 50
1
vote
1
reply
47
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 1 hour ago by
dthorbur
★ 3.0k • written 4 hours ago by
Adrian
• 0
0
votes
1
reply
37
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 40 minutes ago by
GenoMax
151k • written 2 hours ago by
Luwell
• 0
0
votes
1
reply
46
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 2 hours ago by
patrickdm
▴ 260 • written 3 hours ago by
adarsh
▴ 60
1
vote
1
reply
103
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 4 hours ago by
patrickdm
▴ 260 • written 19 hours ago by
andrea
• 0
838
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
0
replies
47
views
HISAT2 or STAR
alignment
hisat2
star
6 hours ago by
Shazel
• 0
0
votes
2
replies
67
views
What to do after fastp?
rna-seq
fastp
alignment
updated 2 hours ago by
dthorbur
★ 3.0k • written 6 hours ago by
Shazel
• 0
1
vote
1
reply
230
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 18 hours ago by
colindaven
7.6k • written 3 days ago by
emil.paulitz
• 0
0
votes
0
replies
72
views
ATAC-seq analysis
atac-seq
hmmratac
calling
peak
macs3
updated 18 hours ago by
GenoMax
151k • written 19 hours ago by
SEJAL
• 0
0
votes
1
reply
123
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 1 day ago by
GenoMax
151k • written 1 day ago by
bn
▴ 30
0
votes
0
replies
123
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Floren
• 0
0
votes
1
reply
457
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 2 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
128
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
2 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.0k
views
normalize between 2 different platform
RNA-Seq
updated 2 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
132
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
bioinformatics
analysis
2 days ago by
linqy
▴ 10
0
votes
1
reply
192
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 2 days ago by
GenoMax
151k • written 2 days ago by
michael.dhar
• 0
2
votes
4
replies
823
views
Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in terms of using repetitive elements to filter peaks
sequence
scatac
cell
single
10xatac
2 days ago by
gynecoloji
• 0
0
votes
2
replies
263
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
2 days ago by
Sd
• 0
0
votes
0
replies
164
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
3 days ago by
a58c4637
• 0
8
votes
5
replies
365
views
nanopore unaligned bam files
nanopore
updated 2 days ago by
GenoMax
151k • written 3 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
153
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
3 days ago by
gogeni5529
▴ 70
0
votes
1
reply
218
views
Issue with Package installation in R.
R
GCC
updated 2 days ago by
GenoMax
151k • written 3 days ago by
harsh
▴ 20
0
votes
0
replies
151
views
MAPQ algorithms of Giraffe
giraffe
vg
3 days ago by
gulin
• 0
5
votes
4
replies
625
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 3 days ago by
colindaven
7.6k • written 11 days ago by
biostars
▴ 30
0
votes
1
reply
202
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 3 days ago by
ATpoint
88k • written 3 days ago by
Vxike
• 0
2
votes
2
replies
1.8k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell
scATAC-Seq
Signac
transcriptomics
updated 3 days ago by
Jan
• 0 • written 3.6 years ago by
patelk26
▴ 340
4
votes
2
replies
267
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
2 days ago by
ATS
▴ 10
1
vote
4
replies
285
views
How to add GFP in STAR reference?
STAR
updated 3 days ago by
GenoMax
151k • written 3 days ago by
bioinfo
▴ 160
0
votes
0
replies
175
views
News:
Population Genomics Using Ancient DNA Data course
DemographicModels
PopulationGenomics
aDNA
Genomics
3 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
215
views
Can you compare GETx and TCGA miRNA non normalized counts a
comapre
to
how
updated 3 days ago by
ATpoint
88k • written 3 days ago by
radwa_noreen
• 0
0
votes
3
replies
332
views
ATAC-seq analysis
ATAC-seq
Samtools
Sorting
updated 4 days ago by
ATpoint
88k • written 4 days ago by
SEJAL
• 0
0
votes
1
reply
248
views
Learn tNGS
tNGS
updated 4 days ago by
GenoMax
151k • written 4 days ago by
hang
• 0
4
votes
3
replies
389
views
Server Requirements for long read data analysis
longreadserver
longreadanalysis
serverrequirements
Server
updated 4 days ago by
colindaven
7.6k • written 5 days ago by
genomics_student
• 0
0
votes
1
reply
250
views
The molecular signatures database (MSigDB) in R
MSigDB
updated 4 days ago by
marco.barr
▴ 170 • written 4 days ago by
Kelly
• 0
2
votes
3
replies
635
views
plotProfile Errors of DiffBind
DiffBind
4 days ago by
lijiangres
▴ 20
0
votes
0
replies
218
views
Job:
Lab Head positions at the WEHI, Melbourne Australia
LabHead
Australia
JobPosting
4 days ago by
Gordon Smyth
★ 8.1k
0
votes
0
replies
204
views
Merging single ATAC seq data sets from multiple sample
10x
4 days ago by
1769mkc
★ 1.3k
1
vote
3
replies
329
views
GSEA analysis in R
R
ranked_list
GSEA
updated 4 days ago by
ATpoint
88k • written 4 days ago by
rajdeepboral00
▴ 70
0
votes
1
reply
250
views
Assembly issues
adapters
Assembly
Spades
updated 4 days ago by
GenoMax
151k • written 4 days ago by
anna
• 0
2
votes
8
replies
540
views
Use taxdb tp get scientific names in local BLAST output
taxdb
sscinames
taxonomy
makeblastdb
blast
updated 4 days ago by
GenoMax
151k • written 6 days ago by
Luca Arbore
▴ 10
1
vote
7
replies
2.5k
views
Search all SRA data for sequence? Raw reads only
SRA
NCBI
Raw reads
fastq
updated 4 days ago by
Wayne
★ 2.1k • written 4.3 years ago by
poppersrules
▴ 10
2
votes
2
replies
317
views
Forum:
Is this Rosalind inspired project actually useful?
python
code-review
4 days ago by
Andrew
• 0
1
vote
1
reply
234
views
Subset a GAM (graph alignment) file
pangenome
vg
vgteam
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Pau
• 0
0
votes
0
replies
216
views
News:
Reproducibility in Bioinformatics course
Conda
Singularity
Docker
Snakemake
Nextflow
4 days ago by
Physalia-courses
★ 2.6k
1
vote
0
replies
255
views
Any tips for optimizing an all vs all alignment with minimap2
mapping
nanopore
genomics
minimap2
4 days ago by
Mark
▴ 60
0
votes
0
replies
216
views
Mismatch in orthology results from local alignment and phylogenetic analysis.
alignment
local
Phylogeny
global
updated 4 days ago by
GenoMax
151k • written 5 days ago by
Shakunthala Natarajan
• 0
4
votes
2
replies
310
views
How to automate blasting contigs?
assembly
contig
blast
WGS
1 day ago by
marongiu.luigi
▴ 740
121,332 results • Page
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Recent Votes
Answer: Quality control metrics in mmCIF
Answer: SNP calling from multiple genomes: No valid SNPs
Comment: Mass-spectrometry proteomics
Comment: Mass-spectrometry proteomics
Answer: Assessing the difference between a de novo assembly and a reference genome
Comment: nanopore unaligned bam files
Answer: How to automate blasting contigs?
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Comment: How to deal with intermediate files
by
dthorbur
★ 3.0k
Fair point about the sensitivity of data. I don't work on human or other particularly sensitive data so never really thought about it.
Comment: How to deal with intermediate files
by
GenoMax
151k
Great list. Globus may be the perfect option, if it is already installed on HPC. Something to consider before using any of the above. Not…
Comment: phage sequence no alignment to genome
by
GenoMax
151k
> StrainA_genome.fasta Is this a publicly available reference genome (preferably RefSeq version) for your organism (strain)? Have you comp…
Answer: How to deal with intermediate files
by
dthorbur
★ 3.0k
There are a bunch of options, and I've seen a lot of different methods over the years. Here are a few of the common ones I've seen/used: …
Answer: Quality control metrics in mmCIF
by
dthorbur
★ 3.0k
There is a lot of useful information in the mmCIF file headers that can be relevant. Each method will have slightly different information a…
Comment: What to do after fastp?
by
dthorbur
★ 3.0k
Please provide more information on what steps you have taken or which workflow you are using. Fastp is a common QC tool, but it's not manda…
Comment: What to do after fastp?
by
AIMAR
▴ 10
Hi you can check this youtube video : [rna seq analysis][1] Even that one as a introduction to RNA seq : [Introduction to RNA-seq][2] Ho…
Comment: Mass-spectrometry proteomics
by
Nasim Gandomdoust
• 0
Thank you for your answer. I conducted an analysis using limpa and found it quite interesting. As far as I understand, both ON and CN model…
Answer: Mitochondrial Annotation Tool
by
patrickdm
▴ 260
Hello, for the annotation you could try [Prokka][1] using the option --kingdom Mitochondria (--gcode 5). Hth. [1]: https://github.com/t…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
Charles Plessy
★ 2.9k
`.command.run: line 304: docker: command not found`: You need either to install the software by yourself, or to let Nextflow download them …
Answer: Assessing the difference between a de novo assembly and a reference genome
by
patrickdm
▴ 260
Hello, you will find informations on dnadiff's output in its documentation's [README][1]; also notice that For more information on t…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
marongiu.luigi
▴ 740
Yes, there was the `--target` parameter missing. I tried again, this time with a `samplesheet.csv` file containing only ``` sample, fasta …
Answer: SNP calling from multiple genomes: No valid SNPs
by
colindaven
7.6k
The typical SNP calling route is to run say 3 short read datasets (fastq input) against one reference genome. Then your approach would like…
Comment: Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
by
GenoMax
151k
https://bioconductor.org/books/3.15/OSCA.intro/index.html is a comprehensive version of scRNAseq analysis. Installation of software would b…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
GenoMax
151k
Usage section for the pipeline: https://nf-co.re/pairgenomealign/2.1.0/docs/usage/ You need to specify a "target" genome using the paramet…
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