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121,194 results • Page
2 of 2424
Sort: Rank
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Votes
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0
votes
0
replies
225
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
6 days ago by
aj
• 0
0
votes
0
replies
219
views
TEtranscripts analysis
TEtranscripts
6 days ago by
frarodmar17
• 0
0
votes
0
replies
214
views
CVNkit call commande
CVNs
CNVKit
Somatic_variant
6 days ago by
AIMAR
▴ 10
0
votes
6
replies
454
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
3 days ago by
n_navy
▴ 10
0
votes
1
reply
270
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq
DEGs
updated 5 days ago by
manaswwm
▴ 570 • written 6 days ago by
noodlejackson
▴ 40
2
votes
3
replies
513
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 6 days ago by
GenoMax
151k • written 16 days ago by
Ambuj
• 0
0
votes
0
replies
187
views
News:
Online course: Introduction to R and Bioconductor
R
Bioconductor
Genomics
6 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
179
views
IM-fusion data analysis
IM-fusion
6 days ago by
frarodmar17
• 0
0
votes
4
replies
350
views
error in reading codelink data
readcodelinkset
4 days ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
250
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 6 days ago by
Aspire
▴ 380 • written 6 days ago by
stalo.lili
• 0
7
votes
5
replies
706
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 5 days ago by
cmdcolin
★ 4.2k • written 21 days ago by
Pierre Lindenbaum
166k
8
votes
6
replies
3.4k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 6 days ago by
GenoMax
151k • written 12.1 years ago by
Mary
11k
1
vote
1
reply
298
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data
Breast-Cancer
TCGA
updated 6 days ago by
Zhenyu Zhang
★ 1.3k • written 9 days ago by
BhagyashreeWaghale
• 0
0
votes
2
replies
336
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 7 days ago by
GenoMax
151k • written 7 days ago by
bioinfo
▴ 150
0
votes
0
replies
202
views
Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV
purity
genome
ploidy
8 days ago by
ting
• 0
10
votes
8
replies
752
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow
workflow
pipeline
8 days ago by
neng
▴ 50
0
votes
1
reply
265
views
What to choose as background in statistic test genetics
test
expression
gene
statistic
updated 7 days ago by
Dunois
★ 2.9k • written 8 days ago by
adigershon8897
• 0
5
votes
4
replies
506
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
updated 8 days ago by
Gordon Smyth
★ 8.1k • written 11 days ago by
n_navy
▴ 10
0
votes
0
replies
469
views
Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics
genetic-variation
epistasis
snp
gnomad
8 days ago by
SonicSoal
• 0
0
votes
0
replies
201
views
Rare variants association analysis (using WGS)
variant
GWAS
rare
WGS
8 days ago by
SeoG
• 0
0
votes
0
replies
209
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat
segmentation
anndata
visiumhd
updated 9 days ago by
GenoMax
151k • written 9 days ago by
npont
• 0
0
votes
0
replies
214
views
News:
Online course -Reproducibility in Bioinformatics - July 7–9
Singularity
Git
Docker
Snakemake
Nextflow
9 days ago by
Physalia-courses
★ 2.6k
1
vote
5
replies
481
views
RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA
rna-sequencing
9 days ago by
h
• 0
0
votes
3
replies
363
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 9 days ago by
GenoMax
151k • written 9 days ago by
Arthur
• 0
1
vote
2
replies
345
views
Pathway enrichment analysis on time-series data by filtering out age comparisons
pea
go
rnaseq
time-series
9 days ago by
fullycratered
• 0
6
votes
8
replies
551
views
building snpeff database for plant
plant
updated 5 days ago by
lieven.sterck
15k • written 9 days ago by
analyst
▴ 60
1
vote
1
reply
253
views
How to find motif in specific region
motif
chip-seq
updated 9 days ago by
Alex Reynolds
36k • written 9 days ago by
zhang616123
• 0
0
votes
0
replies
235
views
How to interpret perplexing qcovhsp result in blastx
blastx
qcovhsp
blastn
9 days ago by
samuel.himes
• 0
0
votes
0
replies
198
views
Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF
bcftools
9 days ago by
Mwangana
• 0
0
votes
0
replies
215
views
Best Practices for Integrating RNA-seq Time Series from Multiple Studies with Varying Protocols
differential-expression
meta-analysis
integration
RNA-seq
time-series
10 days ago by
enee
▴ 20
10
votes
9
replies
5.0k
views
bcftools query add header
bcftools
updated 10 days ago by
GenoMax
151k • written 3.1 years ago by
User000
▴ 750
0
votes
2
replies
394
views
Alternative to PASApipeline
transcriptomics
annotation
updated 9 days ago by
colindaven
7.4k • written 11 days ago by
lagartija
▴ 160
0
votes
0
replies
212
views
How to Get a Genetic Map, Given the Physical Position and Genotype Data of Markers
genetic-map
updated 9 days ago by
Ram
45k • written 10 days ago by
Daniyal
• 0
1
vote
7
replies
2.5k
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 10 days ago by
Michael
55k • written 2.4 years ago by
elizabeth
• 0
1
vote
3
replies
373
views
HISAT2 with Cleaned Data
HISAT2
RNASeq
updated 6 days ago by
lieven.sterck
15k • written 10 days ago by
Gordonz9494
▴ 10
4
votes
1
reply
303
views
Definitions for "differential expression" and "differential abundance" in RNA-seq?
rna-seq
deseq
abundance
differential-expression
updated 9 days ago by
Ram
45k • written 10 days ago by
tw_140
• 0
2
votes
5
replies
450
views
Efficiently find regions in bed file that are within start and end regions of another bed file.
intersect
bedtools
updated 9 days ago by
Alex Reynolds
36k • written 11 days ago by
rxs1018
• 0
2
votes
4
replies
386
views
16S Libraries With Non-Purified Short Fragments
Sequencing
16S
Libraries
Magnetic
Beads
10 days ago by
alenew.am
▴ 10
0
votes
1
reply
285
views
How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq
cell
polyA
single
updated 11 days ago by
GenoMax
151k • written 11 days ago by
Ana
▴ 10
7
votes
6
replies
5.0k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2
ChIP-Seq
ChromHMM
MACS2
CHROMHMM
updated 11 days ago by
luminea
▴ 10 • written 5.9 years ago by
m.sadman.sakib
▴ 120
4
votes
5
replies
551
views
Editing and Adding to a GTF file
Annotation
Gene-ID
GTF
updated 9 days ago by
Ram
45k • written 12 days ago by
Keem Uarren Eiryll
▴ 10
4
votes
2
replies
303
views
Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM
bam
averag
updated 11 days ago by
ATpoint
88k • written 11 days ago by
luminea
▴ 10
3
votes
3
replies
510
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 11 days ago by
colindaven
7.4k • written 16 days ago by
vikasmh111
• 0
0
votes
0
replies
206
views
News:
online course: Introduction to Genome Annotation
Gene-Prediction
Genome-Annotation
Gene-Models
11 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
1.4k
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct
metawrap
module
11 days ago by
shevch2009
• 0
6
votes
7
replies
562
views
Circular heatmap using circos.heatmap in R
R
circos
heatmap
circularheatmap
updated 10 days ago by
GenoMax
151k • written 11 days ago by
Yukta
• 0
0
votes
0
replies
230
views
Zebrafish phenotype ontology enrichment analyses
ontology
zebrafish
11 days ago by
Li
• 0
0
votes
2
replies
322
views
Sequence Duplication for Single-End 3RAD Data
duplication
reduced-representation
10 days ago by
Sarah
• 0
0
votes
0
replies
231
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
11 days ago by
Adrian
• 0
1
vote
6
replies
1.2k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 11 days ago by
Ram
45k • written 10 months ago by
guioliveirareis
▴ 10
121,194 results • Page
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Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
Copy Number Variants with CNVKit
Answer: Detection SNPs and Indels Bacteria
Answer: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
Several errors in DROP Workflow
Single probe id for multiple genes in Microarray
Single probe id for multiple genes in Microarray
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Recent Replies
Comment: Perturb seq
by
GenoMax
151k
While you wait for answers a search brought up this analysis workflow: https://satijalab.github.io/Mixscale/
Comment: Facing issue with output of nextflow pipeline
by
colindaven
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Yeah, this looks like a hack.This page has more standard patterns - https://nextflow-io.github.io/patterns/ - You don't need the `mkdir` …
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
CHOCADAPASSADAEMCHOQ
• 0
Thank you so much!! So kind!
Comment: Analysing Problem Seen In MEGA X
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I'm also facing the same issue. Have you been able to find a way to fix it?
Comment: How to visualize Combat-seq corrected counts
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Sorry, I accidentally used ComBat! ComBat-seq did not produce negative counts. Thanks for all the help!
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Keep in mind for RNASeq 1) if the library was done properly, it's very unlikely you have many fragments shorter than your read length. …
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>de novo assembled 110 reference-grade genomes for cultivated Setaria accessions this type of routine de novo assembly of genomes is aweso…
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It looks hacky. Maybe it "works" but should not be taken as inspiration I guess. Are you sure output could be redicted to other processed l…
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151k
Have you considered the possibility that if no strains of Acinetobacter guillouiae available in NCBI show presence of nitrogen fixing genes…
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This is a common issue that many learners encounter when working with Nextflow output management. 1. Use publishDir("${params.outdir}/..…
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As with any visualisation method, there is a time and a place for them. They are often misused, or used when a different method would be be…
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Your first paragraph is answering the latter and as said in the second paragraph, one cannot force people not to use it. It is like RPKM/F…
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I'm unfamiliar with the representation of phytochemicals in either database, so can't answer for certain, but generally I would say both da…
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There is no answer to this. Some people will say 10, other 3, others 500. Generally, since single-cell is noisy and has dropouts, even for …
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