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120,901 results • Page
1 of 2419
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Votes
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0
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14
views
How label Group list after integratin scRNA-seq and scATAC-seq data
ArchR
1 hour ago by
Bioinformatics_16
• 0
0
votes
0
replies
33
views
Questions on what to focus on in the next 3-4 years of my research
Career
path
3 hours ago by
Abiodun
• 0
835
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
4
replies
202
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
updated 4 hours ago by
GenoMax
150k • written 1 day ago by
himanshu0102
• 0
1
vote
2
replies
130
views
WGS for CNV and Aneuploidy analysis
CNV
Aneuploidy
WGS
updated 10 hours ago by
colindaven
7.4k • written 18 hours ago by
bioinfo1990
▴ 10
0
votes
0
replies
60
views
News:
Course: Phylogenetic Comparative Methods in R – May 12–16 (Online)
PhylogeneticComparativeMethods
UltrametricPhylogenies
R
18 hours ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
149
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
455
views
Issues with T2T in pigeon prepare from isoseq
isoseq
long
rna-seq
read
updated 1 day ago by
anbayega
• 0 • written 6 months ago by
SethJ
• 0
1
vote
1
reply
242
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
293
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
447
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 2 days ago by
mmhryc
• 0 • written 4 days ago by
harsh
▴ 20
1
vote
2
replies
221
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 2 days ago by
Sophia
• 0
3
votes
5
replies
355
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 2 days ago by
Billy Rowell
▴ 500 • written 2 days ago by
jahnreinhard.ringger
• 0
1
vote
12
replies
480
views
MultiQC_report
content_multiqc_fastqc
Quality_control_
Adapter
updated 2 days ago by
GenoMax
150k • written 2 days ago by
AIMAR
• 0
2
votes
2
replies
230
views
Forum:
How to get into research for an absolute beginners
research
updated 2 days ago by
GenoMax
150k • written 2 days ago by
jpeduprep
• 0
0
votes
0
replies
132
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
2 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
211
views
how to do a corellation analysis of multiple CRISPR data sets
batch-effect.
crispr
screen
correlation
2 days ago by
Assa Yeroslaviz
★ 1.9k
8
votes
4
replies
447
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 2 days ago by
LauferVA
4.7k • written 5 days ago by
shpak.max
▴ 60
1
vote
10
replies
501
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 10 hours ago by
colindaven
7.4k • written 3 days ago by
Will
• 0
0
votes
0
replies
169
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
opportunity
postdoc
3 days ago by
Sophie
• 0
1
vote
3
replies
315
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
213
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 2 days ago by
zx8754
12k • written 3 days ago by
ohtang7
▴ 40
0
votes
0
replies
169
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
3 days ago by
karlensberg
• 0
0
votes
9
replies
501
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
236
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
3 days ago by
Franck
• 0
0
votes
0
replies
155
views
Need help defining a threshold
DAVID
Genes
GO
3 days ago by
Ana
• 0
5
votes
9
replies
565
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
updated 2 days ago by
colindaven
7.4k • written 4 days ago by
alexandrakortsi
• 0
5
votes
4
replies
323
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 3 days ago by
ATpoint
87k • written 3 days ago by
maplewj
▴ 20
0
votes
1
reply
388
views
Question about `vg construct`
vg
updated 3 days ago by
Jouni Sirén
▴ 630 • written 8 days ago by
zhengluo
• 0
0
votes
0
replies
175
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
4 days ago by
雨
▴ 20
0
votes
2
replies
743
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
3 days ago by
buffealo
▴ 130
1
vote
8
replies
1.6k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 3 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
400
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
4 days ago by
dk7258859
• 0
0
votes
1
reply
263
views
MULTIQC for miRNAseq data
multiqc
updated 4 days ago by
i.sudbery
21k • written 5 days ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
300
views
How to improve the mapping rate of vg giraffe
vg
updated 4 days ago by
colindaven
7.4k • written 5 days ago by
gulin
• 0
0
votes
6
replies
453
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
1 day ago by
paulanavarrete116
• 0
2
votes
2
replies
365
views
Issues with vg surject into paths
vg
updated 4 days ago by
GenoMax
150k • written 5 days ago by
Rugare
• 0
8
votes
12
replies
605
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 4 days ago by
LauferVA
4.7k • written 5 days ago by
ka132
▴ 10
0
votes
3
replies
309
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
309
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
4 days ago by
Diego
▴ 110
1
vote
1
reply
239
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
351
views
Checking sex of a sample with sequencing data
ATAC-seq
3 days ago by
xqyn
▴ 30
1
vote
5
replies
532
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 5 days ago by
Istvan Albert
102k • written 7 days ago by
shu8
• 0
1
vote
1
reply
253
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 5 days ago by
i.sudbery
21k • written 5 days ago by
ATS
• 0
2
votes
2
replies
413
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 3 days ago by
lieven.sterck
15k • written 8 days ago by
Jl
• 0
1
vote
5
replies
390
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 2 days ago by
Istvan Albert
102k • written 5 days ago by
Ana
• 0
0
votes
1
reply
257
views
cant make the correct matrix
logfc
csv
updated 5 days ago by
lieven.sterck
15k • written 5 days ago by
Naila
• 0
1
vote
4
replies
337
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
5 days ago by
SomeOne
▴ 170
1
vote
7
replies
441
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 5 days ago by
yura.grabovska
▴ 760 • written 5 days ago by
zhang616123
• 0
120,901 results • Page
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Understanding percent spliced in
Understanding percent spliced in
Calculate Percent Spliced In (PSI)
Answer: Merge and unique multiple complete sam files from identical fastq files
Comment: WGS for CNV and Aneuploidy analysis
Answer: How to obtain TPM data after batch effect correction from count data obtained us
Answer: Merge and unique multiple complete sam files from identical fastq files
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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`?
Comment: Error in importing data from 10x genomics into RStudio
by
himanshu0102
• 0
I am using the Seurat package for scRNA seq analysis. I am following this link: https://biostatsquid.com/scrnaseq-preprocessing-work…
Comment: Error in importing data from 10x genomics into RStudio
by
1769mkc
★ 1.2k
can you cite the data set which one you trying?
Comment: Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
by
colindaven
7.4k
I wonder how long it will be till it gets (rightly?) banned by all funding providers. 1 month, 2, maybe 6 ? In a few more years, AI will be…
Comment: WGS for CNV and Aneuploidy analysis
by
colindaven
7.4k
"how many million cells" - are you talking WGS or single cell scWGS ?
Comment: WGS for CNV and Aneuploidy analysis
by
GenoMax
150k
While you wait for answers this should get to started: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-023-01703-8<br> htt…
Comment: Error in importing data from 10x genomics into RStudio
by
GenoMax
150k
Please post exact code/packages you are using. It is unclear what you are doing at this time.
Answer: Merge and unique multiple complete sam files from identical fastq files
by
Pierre Lindenbaum
165k
I wrote https://jvarkit.readthedocs.io/en/latest/SamRemoveDuplicatedNames/ this program just removes the duplicated name+flag but doesn't …
Comment: miRNA-seq normalization
by
paulanavarrete116
• 0
I'm not sure about your question. The 3' adapters were removed in the first step of the workflow using miRDeep2 mapper which allows for rem…
Comment: Issues with T2T in pigeon prepare from isoseq
by
anbayega
• 0
Got the same error using T2T. I will wait to see if there's a quick fix.
Comment: Extract length of sample sequence from vcf
by
Billy Rowell
▴ 500
If you don't want to mess with compiling bleeding-edge bcftools, you could write the same thing in awk. There's no need to filter out the …
Answer: How to obtain TPM data after batch effect correction from count data obtained us
by
Gordon Smyth
★ 7.9k
I would be using divided counts for transcript-level analyses from RSEM, and using log-CPM from the divided counts for clustering, for the …
Answer: Missing short indels from vcf
by
LauferVA
4.7k
Hey @kbranger , IIUC, you have a ~7 bp deletion visible in IGV (with a 7D CIGAR string and ~17–20× depth) that disappears after bcftools…
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