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116,444 results • Page
1 of 2329
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assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 28 minutes ago by
GenoMax
141k • written 35 minutes ago by
ycts
• 0
1
vote
3
replies
169
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 1 hour ago by
swbarnes2
14k • written 4 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
110
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 3 hours ago by
LChart
3.9k • written 4 hours ago by
George
▴ 10
0
votes
0
replies
40
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 2 hours ago by
Ram
43k • written 3 hours ago by
otieno43
▴ 20
0
votes
1
reply
102
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 3 hours ago by
GenoMax
141k • written 3 hours ago by
Kai Xin
• 0
1
vote
1
reply
101
views
Retrieve a % coverage for each transcript
RNA-seq
updated 4 hours ago by
Ram
43k • written 4 hours ago by
jammydodger123456
▴ 40
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
235
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 4 hours ago by
Klaus S
▴ 150 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
1
reply
114
views
How can I solve this error?
metal
updated 4 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 4 hours ago by
GenoMax
141k • written 5 hours ago by
srimmer
• 0
1
vote
2
replies
143
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 4 hours ago by
Ram
43k • written 5 hours ago by
aniigodwinn
• 0
0
votes
2
replies
147
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
updated 5 hours ago by
colindaven
6.3k • written 10 hours ago by
valentinatsar
• 0
1
vote
3
replies
148
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 5 hours ago by
Michael
54k • written 6 hours ago by
LDT
▴ 330
0
votes
8
replies
287
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 4 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
me
• 0
0
votes
1
reply
186
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 8 hours ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
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
8 hours ago by
Ronin
• 0
4
votes
2
replies
1.6k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 10 hours ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
0
votes
3
replies
167
views
Removing duplicates
duplicates
ONT
minimap2
updated 7 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 9 hours ago by
DKA
▴ 40 • written 11 hours ago by
james.melhorn
• 0
0
votes
3
replies
156
views
biomaRt error for different R version
biomaRt
R
updated 7 hours ago by
Mike Smith
★ 2.0k • written 11 hours ago by
manaswwm
▴ 490
0
votes
1
reply
90
views
Freyja plot error
Freyja
updated 6 hours ago by
Ram
43k • written 11 hours ago by
Adyasha
• 0
1
vote
2
replies
106
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
12 hours ago by
hagl
▴ 10
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
105
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
1
reply
119
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 12 hours ago by
Michael
54k • written 13 hours ago by
jonrkarr
▴ 100
0
votes
2
replies
126
views
Bedmethyl file format
bedmethyl
methylation
updated 9 hours ago by
GenoMax
141k • written 13 hours ago by
njornet
▴ 20
0
votes
0
replies
77
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
10 hours ago by
mropri
▴ 150
0
votes
1
reply
144
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 4 hours ago by
bk11
★ 2.3k • written 21 hours ago by
航太郎
• 0
5
votes
4
replies
2.7k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 21 hours ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
537
views
Piping samtools to R
R
NGS
bash
samtools
20 hours ago by
joe
▴ 490
2
votes
2
replies
173
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
bgbs
• 0
3
votes
7
replies
332
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
1 day ago by
ntsopoul
▴ 60
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
3
votes
3
replies
345
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
20 hours ago by
ayushm64
• 0
0
votes
0
replies
92
views
what exactly is a k-mer table (remora)?
remora
basecall
1 day ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 1 day ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
301
views
Rename multiple fastq.gz files
fastq
next-gen
updated 1 day ago by
shenwei356
8.4k • written 1 day ago by
Jérémie
• 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
119
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
1 day ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
200
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 1 day ago by
GenoMax
141k • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
109
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
95
views
GWAS Phenotypes
GWAS
1 day ago by
solomoncharles77
▴ 90
4
votes
2
replies
212
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 1 day ago by
Ram
43k • written 1 day ago by
Adi
▴ 10
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
1
vote
2
replies
225
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 1 day ago by
Joe
21k • written 2 days ago by
ferdinand
▴ 10
0
votes
2
replies
318
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
5 hours ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
309
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 1 day ago by
Ram
43k • written 1 day ago by
Spring
• 0
116,444 results • Page
1 of 2329
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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