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120,910 results • Page
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2
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20
views
Discrepancy between positions on IGV and NCBI's PrimerBLAST
igv
primer
blast
4 minutes ago by
Rozita
▴ 40
0
votes
0
replies
21
views
Why does Radian run so much slower than vanilla R?
R
Python
Radian
VS-Code
1 hour ago by
RR
• 0
3
votes
6
replies
132
views
6 follow
About the Tool FASTP
Preprocessing_Raw
Quality_control_
reads
updated 10 minutes ago by
GenoMax
150k • written 7 hours ago by
AIMAR
• 0
0
votes
0
replies
13
views
Significant SNPs with the same effect in FarmCPU
effect-size
gwas
FarmCPU
likage-disequilibrium
1 hour ago by
AndrMod
• 0
6
votes
11
replies
643
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
3 hours ago by
alexandrakortsi
• 0
0
votes
0
replies
33
views
Job:
Postdoc ML/AI in Genomics & Bioinformatics at Duke University
Postodoc
Genomics
AI
3 hours ago by
alwayshope
▴ 40
0
votes
1
reply
65
views
analyze gene expression of 3 genes in RNA-Seq data
R
RNA-Seq
updated just now by
ATpoint
87k • written 3 hours ago by
pinheirofabiano
▴ 100
1
vote
1
reply
320
views
methRead takes too long
MethylKit
updated 5 hours ago by
Alexander Blume
▴ 10 • written 7 months ago by
CTLong
▴ 140
0
votes
0
replies
42
views
rrvgo::getGoSize error
terms
ReViGO
rrvgo
GO
updated 2 hours ago by
GenoMax
150k • written 5 hours ago by
Ana
• 0
836
votes
169
replies
172k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
42
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
6 hours ago by
Ahmed Jaber
• 0
0
votes
1
reply
81
views
Identifying domain of long-read assembled contig
longread
taxonomy
identification
contig
updated 6 hours ago by
lieven.sterck
15k • written 9 hours ago by
Gio
• 0
0
votes
0
replies
58
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
12 hours ago by
Bioinformatics_16
• 0
0
votes
1
reply
116
views
Forum:
Questions on what to focus on in the next 3-4 years of my research
Career
offtopic
path
updated 10 hours ago by
Michael
55k • written 15 hours ago by
Abiodun
• 0
0
votes
4
replies
262
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
updated 15 hours ago by
GenoMax
150k • written 1 day ago by
himanshu0102
• 0
1
vote
2
replies
154
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
updated 21 hours ago by
colindaven
7.4k • written 1 day ago by
bioinfo1990
▴ 10
0
votes
0
replies
74
views
News:
Course: Phylogenetic Comparative Methods in R – May 12–16 (Online)
PhylogeneticComparativeMethods
UltrametricPhylogenies
R
1 day ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
202
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
4 hours ago by
JustinZhang
▴ 120
0
votes
1
reply
474
views
Issues with T2T in pigeon prepare from isoseq
isoseq
long
rna-seq
read
updated 2 days ago by
anbayega
• 0 • written 6 months ago by
SethJ
• 0
1
vote
1
reply
267
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
updated 2 days ago by
Gordon Smyth
★ 7.9k • written 2 days ago by
Apprentice
▴ 170
1
vote
1
reply
313
views
Missing short indels from vcf
bcftools
shortindels
mpileup
updated 2 days ago by
LauferVA
4.7k • written 5 days ago by
kbranger
• 0
4
votes
6
replies
483
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 2 days ago by
mmhryc
• 0 • written 5 days ago by
harsh
▴ 20
1
vote
2
replies
240
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 2 days ago by
5heikki
11k • written 3 days ago by
Sophia
• 0
4
votes
5
replies
391
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 2 days ago by
Billy Rowell
▴ 510 • written 3 days ago by
jahnreinhard.ringger
• 0
1
vote
12
replies
520
views
MultiQC_report
content_multiqc_fastqc
Quality_control_
Adapter
updated 2 days ago by
GenoMax
150k • written 3 days ago by
AIMAR
• 0
4
votes
3
replies
284
views
Forum:
How to get into research for an absolute beginners
research
updated 6 hours ago by
Yugan Gogul Muthukumar
▴ 10 • written 3 days ago by
jpeduprep
• 0
0
votes
0
replies
149
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
3 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
229
views
how to do a corellation analysis of multiple CRISPR data sets
batch-effect.
crispr
screen
correlation
3 days ago by
Assa Yeroslaviz
★ 1.9k
8
votes
4
replies
466
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 3 days ago by
LauferVA
4.7k • written 5 days ago by
shpak.max
▴ 60
1
vote
10
replies
546
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 21 hours ago by
colindaven
7.4k • written 3 days ago by
Will
• 0
0
votes
0
replies
188
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
opportunity
postdoc
3 days ago by
Sophie
• 0
1
vote
3
replies
339
views
Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
updated 2 days ago by
1769mkc
★ 1.2k • written 3 days ago by
Alex
• 0
0
votes
1
reply
232
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 3 days ago by
zx8754
12k • written 4 days ago by
ohtang7
▴ 40
1
vote
1
reply
222
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
updated 8 hours ago by
ATpoint
87k • written 4 days ago by
karlensberg
• 0
2
votes
9
replies
545
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 4 days ago by
Pierre Lindenbaum
165k • written 5 days ago by
totoroGirl
• 0
1
vote
1
reply
249
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
4 days ago by
Franck
• 0
0
votes
0
replies
169
views
Need help defining a threshold
DAVID
Genes
GO
4 days ago by
Ana
• 0
5
votes
4
replies
343
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 4 days ago by
ATpoint
87k • written 4 days ago by
maplewj
▴ 20
0
votes
1
reply
400
views
Question about `vg construct`
vg
updated 4 days ago by
Jouni Sirén
▴ 630 • written 9 days ago by
zhengluo
• 0
0
votes
0
replies
189
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
4 days ago by
雨
▴ 20
0
votes
3
replies
869
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
2 hours ago by
buffealo
▴ 130
1
vote
8
replies
1.7k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 4 days ago by
lieven.sterck
15k • written 13 months ago by
Matt
• 0
80
votes
32
replies
31k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 days ago by
Paulo
▴ 10 • written 11.2 years ago by
Istvan Albert
102k
1
vote
4
replies
422
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
5 days ago by
dk7258859
• 0
0
votes
1
reply
278
views
MULTIQC for miRNAseq data
multiqc
updated 5 days ago by
i.sudbery
21k • written 5 days ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
319
views
How to improve the mapping rate of vg giraffe
vg
updated 5 days ago by
colindaven
7.4k • written 5 days ago by
gulin
• 0
0
votes
6
replies
481
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
2 days ago by
paulanavarrete116
• 0
2
votes
2
replies
382
views
Issues with vg surject into paths
vg
updated 5 days ago by
GenoMax
150k • written 6 days ago by
Rugare
• 0
8
votes
12
replies
625
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 5 days ago by
LauferVA
4.7k • written 5 days ago by
ka132
▴ 10
0
votes
3
replies
321
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 5 days ago by
GenoMax
150k • written 5 days ago by
bge
• 0
120,910 results • Page
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Answer: Find the reads which correspond to DP of vcf
Answer: Find the reads which correspond to DP of vcf
High BCV in differential expression, thoughts?
Comment: About the Tool FASTP
Comment: About the Tool FASTP
Answer: About the Tool FASTP
C: Fetching Genbank Assembly IDs with protein
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Comment: Discrepancy between positions on IGV and NCBI's PrimerBLAST
by
Rozita
▴ 40
On IGV, it shows that the primer is spanning the promoter region, whereas in PrimerBLAST it is showing that it is spanning an intron in the…
Comment: Discrepancy between positions on IGV and NCBI's PrimerBLAST
by
GenoMax
150k
It is difficult to see what you want to illustrate from the screenshot attached. Can you explain what is fhe difference that you are observ…
Comment: About the Tool FASTP
by
GenoMax
150k
As others have indicated don't overthink this part of analysis. You don't need to change default parameters unless you have a very specific…
Comment: About the Tool FASTP
by
GenoMax
150k
Please use `ADD REPLY/ADD COMMENT` when responding to existing posts. `SUBMIT ANSWER` is for NEW answers for the original question.
Comment: About the Tool FASTP
by
AIMAR
• 0
Here the command line I've used in my script to preprocess my data (DNA paired-end reads). By preprocess I mean adapter removal, trimming l…
Answer: About the Tool FASTP
by
shelkmike
★ 1.5k
In my experience, for paired end reads Fastp is great with default parameters. For single end reads I suggest to give it the adapter sequen…
Answer: analyze gene expression of 3 genes in RNA-Seq data
by
ATpoint
87k
You should analyze the full dataset using standard workflows such as limma-voom or DESeq2 and then get the stats for the relevant genes by …
Comment: DiffBind normalization error: invalid argument type (list) - cannot make it work
by
buffealo
▴ 130
@rory, I tried several variations, and I am getting these errors. These errors also occurred when I tried with the metadata files I wrote a…
Comment: Larger genome size than expected-please help
by
colindaven
7.4k
You can try inspector for that - https://github.com/Maggi-Chen/Inspector
Comment: Larger genome size than expected-please help
by
alexandrakortsi
• 0
Thank you all for the advice!! My assembly has 66 contigs. I found someone that had a similar situation and his advice was to map reads to …
Comment: Online Training - Analysis of Transposable elements
by
Samuel Lampa
★ 1.3k
Hi! Super interesting! Is there any chance you will give another session of this course?
Answer: methRead takes too long
by
Alexander Blume
▴ 10
You are passing a list of data.table objects (loaded via fread) into methRead(): coverage_fread <- lapply(coverage_files, fread) …
Comment: About the Tool FASTP
by
ATpoint
87k
"better" means current is not good. Better ask about the underlying problem rather than these open-ended. problems. What is the issue and s…
Comment: About the Tool FASTP
by
Gabriel R.
★ 2.9k
Hey Aimar! Could you be more specific with "pre-processing", fastp can, among other things, remove adapters which is usually a good idea be…
Comment: How to get into research for an absolute beginners
by
Yugan Gogul Muthukumar
▴ 10
Try reading topics which you find interest in and when you have sufficient knowledge, you would know what are the question which are still …
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