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1,000 results • Page
1 of 20
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Votes
Replies
0
votes
1
reply
35
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 59 minutes ago by
GenoMax
141k • written 1 hour ago by
ycts
• 0
0
votes
0
replies
50
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 3 hours ago by
Ram
43k • written 3 hours ago by
otieno43
▴ 20
0
votes
1
reply
116
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 3 hours ago by
GenoMax
141k • written 4 hours ago by
Kai Xin
• 0
1
vote
1
reply
106
views
Retrieve a % coverage for each transcript
RNA-seq
updated 5 hours ago by
Ram
43k • written 5 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
118
views
How can I solve this error?
metal
updated 5 hours ago by
GenoMax
141k • written 5 hours ago by
22211020193
• 0
0
votes
0
replies
59
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 5 hours ago by
GenoMax
141k • written 6 hours ago by
srimmer
• 0
1
vote
2
replies
145
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 4 hours ago by
Ram
43k • written 6 hours ago by
aniigodwinn
• 0
0
votes
0
replies
61
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
9 hours ago by
Ronin
• 0
0
votes
3
replies
193
views
Removing duplicates
duplicates
ONT
minimap2
updated 33 minutes ago by
joe
▴ 490 • written 10 hours ago by
quentinperriere
• 0
0
votes
1
reply
103
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 10 hours ago by
DKA
▴ 40 • written 11 hours ago by
james.melhorn
• 0
0
votes
1
reply
90
views
Freyja plot error
Freyja
updated 6 hours ago by
Ram
43k • written 12 hours ago by
Adyasha
• 0
0
votes
0
replies
58
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
13 hours ago by
chemokine-1
▴ 10
0
votes
1
reply
118
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
updated 3 hours ago by
LChart
3.9k • written 13 hours ago by
feather-W
• 0
0
votes
2
replies
126
views
Bedmethyl file format
bedmethyl
methylation
updated 10 hours ago by
GenoMax
141k • written 14 hours ago by
njornet
▴ 20
0
votes
0
replies
78
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
14 hours ago by
Ali
• 0
2
votes
4
replies
223
views
SnpEff annotates coding duplication as intronic?
snpeff
16 hours ago by
kirill.zaslavsky
• 0
0
votes
2
replies
144
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
11 hours ago by
mropri
▴ 150
0
votes
1
reply
150
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 5 hours ago by
bk11
★ 2.3k • written 21 hours ago by
航太郎
• 0
0
votes
0
replies
86
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
1 day ago by
shasabhi1
• 0
0
votes
0
replies
82
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
1 day ago by
Nishat
• 0
0
votes
0
replies
92
views
what exactly is a k-mer table (remora)?
remora
basecall
1 day ago by
anne
• 0
1
vote
1
reply
125
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
dsull
★ 5.8k • written 1 day ago by
niruf
• 0
0
votes
0
replies
95
views
GWAS Phenotypes
GWAS
1 day ago by
solomoncharles77
▴ 90
0
votes
1
reply
164
views
GSEA analysis in R
GSEA
R
Arabidopsis
updated 1 day ago by
sansan_96
▴ 80 • written 1 day ago by
Sudip
• 0
0
votes
0
replies
96
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
1 day ago by
QX
• 0
2
votes
5
replies
310
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
15 hours ago by
Bikram Kumar
• 0
0
votes
2
replies
212
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
David
• 0
1
vote
2
replies
220
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
1
reply
157
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
sinhas
• 0
0
votes
1
reply
179
views
merging Seurat objects after SCT
Seurat
SCT
updated 2 days ago by
Ram
43k • written 2 days ago by
michelle.swarovski
• 0
0
votes
1
reply
152
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 2 days ago by
GenoMax
141k • written 2 days ago by
haiying.kong
▴ 360
0
votes
2
replies
225
views
RNAseq 1 control 2 different treatment
RNA-seq
1 day ago by
matteo.levorato
• 0
1
vote
0
replies
113
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
0
votes
0
replies
121
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
GenoMax
141k • written 2 days ago by
bioinfo
▴ 150
2
votes
0
replies
166
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
2 days ago by
Alexander
▴ 220
1
vote
1
reply
149
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 2 days ago by
GenoMax
141k • written 2 days ago by
eesiribloom
▴ 80
0
votes
0
replies
107
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
2 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
111
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
2 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
125
views
FreeBayes detection capacity
reads
freebayes
long
2 days ago by
quentinperriere
• 0
0
votes
2
replies
195
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
10 hours ago by
DKA
▴ 40
0
votes
2
replies
223
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
2 days ago by
rj.rezwan
• 0
0
votes
0
replies
143
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
3 days ago by
Hien
• 0
0
votes
2
replies
252
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
1 day ago by
Koketso
• 0
0
votes
0
replies
173
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 3 days ago by
Ram
43k • written 3 days ago by
menyawino
• 0
1
vote
3
replies
295
views
Ensembl gene id conversion
biomart
ensembl
updated 1 day ago by
ATpoint
81k • written 3 days ago by
naveedhasan2000
• 0
1
vote
2
replies
283
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Jiang
• 0
0
votes
0
replies
169
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
4 days ago by
YiweiZhu
▴ 30
0
votes
0
replies
174
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 3 days ago by
Ram
43k • written 4 days ago by
anitharavichandran2211
• 0
0
votes
1
reply
216
views
Ciriquant not configuring hisat2 indexed files
ciriquant
updated 4 days ago by
Carlo Yague
8.6k • written 4 days ago by
Atul K.
• 0
0
votes
2
replies
291
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
4 days ago by
O.rka
▴ 710
1,000 results • Page
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Recent Votes
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
C: What is the definition of "read depth" vs "coverage"? (again...)
C: What is the definition of "read depth" vs "coverage"? (again...)
Comment: Bwa sampe - BGI
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Tools To Calculate Average Coverage For A Bam File?
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Comment: Per base sequence content failed miserably
by
GenoMax
141k
What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
I guess the enlightening question is: duplicates of what?
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
Comment: Supergnova stuck in tutorial
by
Murat
• 0
Hi Gerard, I am also using the tutorial and found your answer. The ftp links are not working any longer; is there any other source to downl…
Comment: Method to detect genome doubling
by
Zhenyu Zhang
★ 1.2k
This is only true for pure WGD that is not distinguishable using NGS. However, in most tumor evolution, a WGD event is often followed b…
Comment: Questions about a bug when transferring cram file to bam file
by
Pierre Lindenbaum
161k
> Interesting, does this mean I cannot find the reference of this cram file? it means that the REF you're using is not the one that was …
Comment: How to get the reference panel for UKBB
by
bk11
★ 2.3k
Please check this link [here][1]: ![https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/genetic-data][2] [1]: https://www.…
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