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121,419 results • Page
1 of 2429
Sort: Rank
Rank
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Votes
Replies
0
votes
3
replies
82
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Host Removal Issues Human/Dog with samples containing Eukaryotic species
Eukarotic
Mapping
Host
3 hours ago by
Jon
• 0
1
vote
3
replies
225
views
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
mRNA
rna-seq
bowtie
alignment
updated 4 hours ago by
swbarnes2
15k • written 19 hours ago by
JourneyToAbyss
▴ 250
0
votes
1
reply
76
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
updated 4 hours ago by
swbarnes2
15k • written 15 hours ago by
Cristina
• 0
1
vote
2
replies
117
views
Venn Diagram
VennDiagram
updated 5 hours ago by
WouterDeCoster
48k • written 15 hours ago by
Nasim Gandomdoust
• 0
840
votes
170
replies
180k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 7 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
1
reply
106
views
Questions about sample_accession_id and file_accession_id from EGA files
EGA
open
WGS
data
updated 14 hours ago by
GenoMax
152k • written 21 hours ago by
askif4
▴ 20
4
votes
3
replies
205
views
Example of ClinVar pathogenic variant where the reference allele is pathogenic?
snp
variant
pathogenic
clinvar
updated 1 day ago by
GenoMax
152k • written 1 day ago by
a615ebfb
▴ 60
0
votes
1
reply
116
views
Functional Analysis Using EMU Output – Has Anyone Tried This?
emu
updated 1 day ago by
andres.firrincieli
3.9k • written 1 day ago by
henrique.mouradias
• 0
1
vote
1
reply
126
views
featureCounts -t option not working in v2.0.8?
subread
featureCounts
RNAseq
updated 1 day ago by
rfran010
★ 1.5k • written 1 day ago by
atan
• 0
0
votes
1
reply
128
views
mm10 blacklist regions detailed information
sequencing
DNA
blacklist
updated 1 day ago by
GenoMax
152k • written 1 day ago by
annaA
▴ 10
0
votes
1
reply
127
views
identify unmapped regions
human
illumina
libraries
updated 1 day ago by
GenoMax
152k • written 1 day ago by
María José
▴ 10
0
votes
1
reply
217
views
martCheck - Error - You must provide a valid Mart object - for running HoneyBADGER for CNV computation
CNV
biomaRt
HoneyBADGER
1 day ago by
mete.han.celebi
• 0
0
votes
1
reply
173
views
How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
module
analysis
WGCNA
preservation
updated 1 day ago by
andres.firrincieli
3.9k • written 1 day ago by
Berkan
• 0
0
votes
1
reply
152
views
filters used in mutation discovery from RNAseq data
filter
RNAseq
mutation
updated 1 day ago by
GenoMax
152k • written 1 day ago by
htchd
▴ 20
2
votes
3
replies
271
views
Trouble Using GEO Files with Seurat
seurat
GEO
scRNA
2 days ago by
Jamie
• 0
0
votes
0
replies
131
views
Knowledge Graph for AI
KnowledgeGraph
biotech
AI
SPOKE
Bioinformatician
2 days ago by
Cornelio
• 0
2
votes
2
replies
871
views
How to convert from .spec to .bam?
bam
file-formatting
spec
updated 2 days ago by
Daniel Lai
▴ 10 • written 4.7 years ago by
gmora
▴ 30
2
votes
1
reply
181
views
Insert size is zero
rna-seq
fastp
insert
size
updated 2 days ago by
GenoMax
152k • written 2 days ago by
SpliceAndScript
• 0
0
votes
3
replies
282
views
Should matched samples (not paired) be included in the DESeq2 design model?
edgeR
limma
DESeq2
updated 1 day ago by
i.sudbery
21k • written 2 days ago by
marieke
• 0
0
votes
4
replies
276
views
Trajectory Analysis scRNA-seq with one cell type and two developmental stages
cellrank
palantir
pseudotime-trajectory-analysis
scrna-seq
trajectory-analysis
1 day ago by
npont
▴ 10
0
votes
1
reply
532
views
How to run trajectory analysis with only one cell type using palantir?
palantir
scanpy
updated 2 days ago by
npont
▴ 10 • written 11 months ago by
bioinfo
▴ 160
0
votes
1
reply
165
views
should I remove the transcripts from annotate peak region in ATAC-seq
ATAC-seq
updated 1 day ago by
rfran010
★ 1.5k • written 2 days ago by
QX
▴ 70
3
votes
2
replies
245
views
DESeq2 LRT test with multifactorial design
test
design
multifactorial
LRT
2 days ago by
lessismore
★ 1.4k
1
vote
0
replies
680
views
Tool:
Created a better alternative to clunky gene databases, with functions that are consolidated from various gene databases. It's your one-stop shop for …
browser
export
data
search
gene
2 days ago by
Krish
• 0
1
vote
0
replies
160
views
Tool:
Containerized NGS Data Processing Pipelines
rna-seq
atac-seq
pipeline
chip-seq
docker
3 days ago by
Noah
▴ 10
0
votes
1
reply
184
views
Scvi - Integration
integration
singlecell
scvi
updated 2 days ago by
antonioggsousa
3.3k • written 3 days ago by
t.foskolos
• 0
0
votes
0
replies
157
views
Genotype Imputations Question
vcf
imputations
genomics
3 days ago by
Jonathan
• 0
0
votes
1
reply
197
views
Clarification of options --keep-dup: all vs. -f FRAG in MACS3
human
libraries
illumina
callpeak
macs3
updated 3 days ago by
ATpoint
88k • written 3 days ago by
María José
▴ 10
6
votes
2
replies
492
views
Should I perform integration to correct batch effects?
batch
effect
updated 3 days ago by
antonioggsousa
3.3k • written 7 days ago by
han
▴ 20
2
votes
1
reply
216
views
Batch correction in TNBC epithelial cells
tnbc
seurat
epithelialCells
scRNAseq
BatchEffect
updated 3 days ago by
ATpoint
88k • written 3 days ago by
TNF_alpha
• 0
2
votes
5
replies
454
views
7 follow
Best way to install R packages on an HPC?
R
HPC
updated 4 days ago by
Charles Plessy
★ 2.9k • written 4 days ago by
ChumBucket2024
▴ 10
2
votes
2
replies
275
views
how to use filter_vep to filter vcf file
vcf
filter
3 days ago by
htchd
▴ 20
1
vote
2
replies
266
views
How to interpret genomescope to help remove duplicates
assembly
hifi
genomescope
4 days ago by
mohamadelian1996
• 0
0
votes
2
replies
248
views
Is it valid to stack brightfield and fluorescence channels in a CNN input?
fluorescent-microscopy
imaging
microscopy
updated 4 days ago by
LChart
5.0k • written 4 days ago by
Antonio
• 0
0
votes
0
replies
174
views
FusionCatcher cases where gene1 and gene 2 have 2 matches
fusions
fusioncatcher
4 days ago by
ieie
▴ 20
0
votes
2
replies
255
views
mgl tool index error
docking
molecular
error
3 days ago by
Mahesh
• 0
2
votes
3
replies
353
views
convert raw counts to TPM
R
updated 4 days ago by
dthorbur
★ 3.0k • written 4 days ago by
pinheirofabiano
▴ 130
1
vote
7
replies
399
views
Creating kraken2 custom database
kraken2
updated 4 days ago by
GenoMax
152k • written 4 days ago by
ramiro.barrantes
▴ 60
0
votes
0
replies
179
views
How to determine the coordinate of the transposon insertion on the reverse reading?
Tn-seq
transposon
blastn
4 days ago by
Елизавета
• 0
0
votes
6
replies
406
views
Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
Alevin-Fry
single-cell
sequencing
Salmon
RNA
1 day ago by
wooh
• 0
0
votes
0
replies
181
views
News:
Conservation Genomics course
PopulationGenomics
Ne
ConservationGenomics
4 days ago by
Physalia-courses
★ 2.6k
0
votes
3
replies
327
views
Snakemake Module Error: string indices must be integers
GATK
Snakemake
updated 4 days ago by
Jesse
▴ 870 • written 5 days ago by
andean
• 0
1
vote
3
replies
333
views
How do I generate a Manhattan plot like this?
data-visualization
manhattan-plot
4 days ago by
jianhua.mert
• 0
0
votes
2
replies
334
views
ATAC seq: from peaks to differential analysis ??
MACS2
DESeq2
ATACseq
updated 5 days ago by
rfran010
★ 1.5k • written 5 days ago by
Picasa
▴ 680
1
vote
1
reply
259
views
Where to find expected copy number for a gene
genomics
updated 5 days ago by
GenoMax
152k • written 5 days ago by
LayneSadler
▴ 90
0
votes
4
replies
1.2k
views
Cut&Run replicates handling
peakcaller
replicates
SEACR
chipseq
updated 5 days ago by
schowdhury8950
• 0 • written 12 months ago by
g.anande
• 0
0
votes
1
reply
255
views
Unable to extract count matrices from multi-layered Seurat object
seurat
5 days ago by
bgbs
• 0
21
votes
12
replies
753
views
7 follow
Learning Nextflow
Genomic
Pipeline_analysis
Nextflow
5 days ago by
AIMAR
▴ 40
3
votes
1
reply
336
views
open target platform SNP to Gene qurey
SNPtoGene
GWAS
SNP
updated 6 days ago by
GenoMax
152k • written 6 days ago by
SeoG
▴ 10
0
votes
1
reply
326
views
usage of ChromHMM and Segway
ChromHMM
Segway
updated 5 days ago by
Pierre Lindenbaum
166k • written 6 days ago by
qian
• 0
121,419 results • Page
1 of 2429
Recent Votes
Comment: Venn Diagram
Example of ClinVar pathogenic variant where the reference allele is pathogenic?
Answer: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
Answer: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
Answer: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
Comment: featureCounts -t option not working in v2.0.8?
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Recent Replies
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
• 0
What are your thoughts of first Mapping my target reads at say 95% or higher first, then doing host removal of the remaining reads, and the…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
• 0
Yes, I have read about that tool, as it appeared to be what I was looking for. I tried installing the BBMap on my Windows computer, but c…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
> I can only work with the tools available on Galaxy.org That requirement is likely going to make this very difficult to accomplish, ther…
Answer: Why little difference in RNAseq alignment when flipping forward and reverse stra
by
swbarnes2
15k
Bowtie doesn't know what read should go in what direction. It's aligning to genome, it will just flip things to make the alignment work. …
Answer: DESeq2 design for differential expression with 2 timepoints and 2 controls
by
swbarnes2
15k
Adding interactions is not correct for most of what you are doing. Time + treatment is what you want for 1 and 2. For questions like 3, m…
Comment: Venn Diagram
by
WouterDeCoster
48k
I don't think that is possible. You may have some luck if you look for an Euler diagram instead. But as @lievensterck said, it is just not …
Comment: Venn Diagram
by
lieven.sterck
15k
I don't think there exist any software that will generate this. Personally I would not go above 5-6 , as those higher numbers become reall…
Comment: Why little difference in RNAseq alignment when flipping forward and reverse stra
by
GenoMax
152k
> I ran bowtie2, using bulk paired RNA-seq data, with the forward and reverse strand flipped. If you know you flipped the data then re-do …
Comment: Questions about sample_accession_id and file_accession_id from EGA files
by
GenoMax
152k
Based on the EGA help page there is a way to download the metadata, which should give you more information. > Registered EGA users can dow…
Comment: Why little difference in RNAseq alignment when flipping forward and reverse stra
by
Juke34
9.2k
Did you provide any other parameter related to read orientation ?
Comment: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
GenoMax
152k
It is likely this one --> https://www.ncbi.nlm.nih.gov/clinvar/variation/36924/ From original search here --> https://www.ncbi.nlm.nih.gov…
Comment: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
a615ebfb
▴ 60
Thanks, Jeremy! Not sure if I retrieved the right one but it does not show up as pathogenic on the website: https://www.ncbi.nlm.nih.gov/…
Answer: Example of ClinVar pathogenic variant where the reference allele is pathogenic?
by
Jeremy Leipzig
23k
For REF/REF entries the ALT is '.' wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz gunzip -c "c…
Answer: Functional Analysis Using EMU Output – Has Anyone Tried This?
by
andres.firrincieli
3.9k
You can't use EMU with tools like PICRUSt2 because it doesn't produce typical outputs such as OTUs or ASVs. EMU works more like a read-lev…
Comment: featureCounts -t option not working in v2.0.8?
by
rfran010
★ 1.5k
Try the older version? Is it the same GTF from before? I would guess a formatting issue with the 9th column, but I haven't tried this ver…
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