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120,907 results • Page
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About the Tool FASTP
Preprocessing_Raw
Quality_control_
reads
updated just now by
shelkmike
★ 1.5k • written 5 hours ago by
AIMAR
• 0
5
votes
11
replies
618
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
1 hour ago by
alexandrakortsi
• 0
0
votes
0
replies
17
views
Job:
Postdoc ML/AI in Genomics & Bioinformatics at Duke University
Postodoc
Genomics
AI
1 hour ago by
alwayshope
▴ 40
0
votes
1
reply
32
views
analyze gene expression of 3 genes in RNA-Seq data
R
RNA-Seq
updated 31 minutes ago by
ATpoint
87k • written 1 hour ago by
pinheirofabiano
▴ 100
1
vote
1
reply
312
views
methRead takes too long
MethylKit
updated 3 hours ago by
Alexander Blume
▴ 10 • written 7 months ago by
CTLong
▴ 140
0
votes
0
replies
38
views
rrvgo::getGoSize error
terms
ReViGO
rrvgo
GO
updated 10 minutes ago by
GenoMax
150k • written 3 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
38
views
Genotype Imputation for VCF File via API Using R ?
Genotype-Imputation
VCF
API
4 hours ago by
Ahmed Jaber
• 0
0
votes
1
reply
76
views
Identifying domain of long-read assembled contig
longread
taxonomy
identification
contig
updated 4 hours ago by
lieven.sterck
15k • written 7 hours ago by
Gio
• 0
0
votes
0
replies
55
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
10 hours ago by
Bioinformatics_16
• 0
0
votes
1
reply
111
views
Forum:
Questions on what to focus on in the next 3-4 years of my research
Career
offtopic
path
updated 8 hours ago by
Michael
55k • written 13 hours ago by
Abiodun
• 0
0
votes
4
replies
254
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
updated 13 hours ago by
GenoMax
150k • written 1 day ago by
himanshu0102
• 0
1
vote
2
replies
151
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
updated 19 hours ago by
colindaven
7.4k • written 1 day ago by
bioinfo1990
▴ 10
0
votes
0
replies
72
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
198
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
2 hours ago by
JustinZhang
▴ 120
0
votes
1
reply
472
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
265
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
311
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
479
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
235
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
388
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
515
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
278
views
Forum:
How to get into research for an absolute beginners
research
updated 4 hours ago by
Yugan Gogul Muthukumar
▴ 10 • written 3 days ago by
jpeduprep
• 0
0
votes
0
replies
146
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
226
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
464
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
538
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 19 hours ago by
colindaven
7.4k • written 3 days ago by
Will
• 0
0
votes
0
replies
184
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
opportunity
postdoc
3 days ago by
Sophie
• 0
1
vote
3
replies
335
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
230
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 3 days ago by
zx8754
12k • written 3 days ago by
ohtang7
▴ 40
0
votes
1
reply
216
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
updated 6 hours ago by
ATpoint
87k • written 3 days ago by
karlensberg
• 0
0
votes
9
replies
538
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 3 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
totoroGirl
• 0
1
vote
1
reply
246
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
4 days ago by
Franck
• 0
0
votes
0
replies
167
views
Need help defining a threshold
DAVID
Genes
GO
4 days ago by
Ana
• 0
5
votes
4
replies
340
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
397
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
187
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
848
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
58 minutes 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 2 days ago by
Paulo
▴ 10 • written 11.2 years ago by
Istvan Albert
102k
1
vote
4
replies
420
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
4 days ago by
dk7258859
• 0
0
votes
1
reply
276
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
315
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
477
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
2 days ago by
paulanavarrete116
• 0
2
votes
2
replies
380
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
623
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
319
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 5 days ago by
GenoMax
150k • written 5 days ago by
bge
• 0
0
votes
2
replies
325
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
5 days ago by
Diego
▴ 110
1
vote
1
reply
250
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 5 days ago by
GenoMax
150k • written 5 days ago by
ParastooA
▴ 20
0
votes
4
replies
362
views
Checking sex of a sample with sequencing data
ATAC-seq
4 days ago by
xqyn
▴ 30
120,907 results • Page
1 of 2419
Recent Votes
Answer: methRead takes too long
Comment: Help with error in GATK variant calling
Online Training - Analysis of Transposable elements
The Biostar Handbook. A bioinformatics e-book for beginners.
Comment: How to get into research for an absolute beginners
Comment: How to get into research for an absolute beginners
BWA Alignment
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Comment: 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 …
Comment: Identifying domain of long-read assembled contig
by
lieven.sterck
15k
you can consider running Kraken2 , or perhaps kma (but that is rather on read level )
Comment: PCA comparison of cell line vs tumors
by
ATpoint
87k
I would not put a cell line and primary cells into the same analysis, regardless of the normalization and integration method. Much (or most…
Comment: Questions on what to focus on in the next 3-4 years of my research
by
Michael
55k
This post does not fit the theme of this forum.
Comment: From GCA identifiers, download Genbank file format?
by
cmdcolin
★ 4.2k
thanks, great tool. not sure if there is a way to automatically unzip the ncbi_dataset.zip file that it downloads, but I added "unzip -o nc…
Comment: Merge and unique multiple complete sam files from identical fastq files
by
JustinZhang
▴ 120
The is my current workaround: ```python from argparse import ArgumentParser from pathlib import Path import polars as pl def main(): …
Comment: Error in importing data from 10x genomics into RStudio
by
GenoMax
150k
Are you trying to follow the tutorial you linked? Do you get the error on step 1 that is `import data`?
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