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116,567 results • Page
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0
votes
1
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70
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Seurat merge and batch correction
Seurat
updated 8 minutes ago by
Ram
43k • written 16 hours ago by
sooni
▴ 20
1
vote
1
reply
16
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated just now by
Pierre Lindenbaum
161k • written 28 minutes ago by
Biostar
2.7k
1
vote
1
reply
26
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
heelpPlease
• 0
0
votes
6
replies
582
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 54 minutes ago by
Ram
43k • written 6 months ago by
Gnana
• 0
0
votes
6
replies
65
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
snRNA-seq
STARSolo
scRNA-seq
STAR
15 minutes ago by
atowns21
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
37
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 hour ago by
bk11
★ 2.3k • written 2 hours ago by
alphaflylizard
• 0
2
votes
3
replies
88
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 hours ago by
GenoMax
141k • written 3 hours ago by
Estevão
• 0
0
votes
2
replies
95
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
2 hours ago by
Dylan
• 0
0
votes
1
reply
55
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 3 hours ago by
Pierre Lindenbaum
161k • written 4 hours ago by
Lada
▴ 30
3
votes
10
replies
331
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 3 hours ago by
Ram
43k • written 19 hours ago by
dominickd
• 0
3
votes
7
replies
371
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 2 hours ago by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
0
votes
0
replies
34
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
5 hours ago by
ohtang7
▴ 40
0
votes
0
replies
40
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
5 hours ago by
Kash
▴ 110
2
votes
0
replies
53
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 5 hours ago by
Ram
43k • written 6 hours ago by
carlopecoraro2
★ 2.5k
2
votes
2
replies
352
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 7 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
78
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 7 hours ago by
GenoMax
141k • written 7 hours ago by
Srinka
▴ 20
8
votes
5
replies
4.7k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
4
replies
163
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 5 hours ago by
GenoMax
141k • written 8 hours ago by
njornet
▴ 20
5
votes
3
replies
521
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 8 hours ago by
colindaven
6.4k • written 5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
42
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 5 hours ago by
Ram
43k • written 8 hours ago by
SHREYA
• 0
0
votes
3
replies
313
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 8 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
50
views
Merging replicates from Encode project
CHIP-seq
encode
9 hours ago by
Nurken
• 0
1
vote
3
replies
145
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
10 hours ago by
WouterDeCoster
47k
0
votes
3
replies
145
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 7 hours ago by
mchour
• 0 • written 10 hours ago by
rhossen
• 0
1
vote
1
reply
108
views
WGCNA preservation analysis
WGCNA
preservation
updated 10 hours ago by
Michael
54k • written 12 hours ago by
michael.flower.14
▴ 180
0
votes
2
replies
117
views
some error in building kraken2 database
metagenome
kraken2
updated 5 hours ago by
Ram
43k • written 10 hours ago by
Art1ess
• 0
0
votes
1
reply
80
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 5 hours ago by
bk11
★ 2.3k • written 11 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
84
views
Plots for DNA methylation data
plots
DNA
methylation
updated 9 hours ago by
GenoMax
141k • written 12 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
443
views
python file for coding potential calculator
cpc2.py
updated 13 hours ago by
atharvakarkare14
▴ 10 • written 5 days ago by
Ashok
• 0
1
vote
1
reply
115
views
Failed kmer content
kmer
illumina
ngs
updated 5 hours ago by
Ram
43k • written 14 hours ago by
Kasturi
• 0
0
votes
1
reply
109
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 12 hours ago by
Basti
★ 2.0k • written 15 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
81
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
16 hours ago by
yxwucq
• 0
0
votes
0
replies
51
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 5 hours ago by
Ram
43k • written 16 hours ago by
SSSJec
• 0
0
votes
6
replies
214
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 hour ago by
Sd
• 0
0
votes
2
replies
137
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
1 day ago by
sainavyav22
• 0
0
votes
1
reply
106
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
239
views
Error in cnetplot enrichplot package
R
updated 23 hours ago by
Ram
43k • written 1 day ago by
Farhad
• 0
1
vote
4
replies
170
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Κοσμάς
• 0
0
votes
0
replies
81
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
3
votes
3
replies
144
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
c_u
▴ 520
0
votes
0
replies
67
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 1 day ago by
Ram
43k • written 1 day ago by
sansan_96
▴ 80
0
votes
2
replies
127
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
1 day ago by
dxj294
• 0
0
votes
0
replies
74
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 5 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
118
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 23 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
1
reply
115
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
ATpoint
81k • written 1 day ago by
catherine.teyssier
• 0
2
votes
3
replies
167
views
from row count to tpm
tpm
row-count
normalization
13 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
74
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Abeer
• 0
1
vote
5
replies
176
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
116,567 results • Page
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The Biostar Herald for Tuesday, April 23, 2024
Answer: Including plasmid in transcriptome assemblies
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
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Comment: The Biostar Herald for Tuesday, April 23, 2024
by
Pierre Lindenbaum
161k
bwa 0.7.18 released ! https://github.com/lh3/bwa/releases/tag/v0.7.18
Comment: Downsampling fastq file
by
Ram
43k
I'm moving this to a comment for now.
Answer: Seurat merge and batch correction
by
bk11
★ 2.3k
You can merge your seven Seurat objects and perform integration using **Seurat V5** to remove the batch effect- ```r library(Seurat) libra…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Yeah, I've been digging around the web for a while now. Can't find any information about the barcodes. The total number of combinations is …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Ah I see that in now. I am not sure why MGI has split the whitelist into two sections. You may need to see if you can dig up some info abou…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
read 1 is 30bp... which I think you meant to type. If you scroll approximately halfway down the json file I linked to, it has the following…
Comment: TCGA2STAT Error: Firehose connection
by
Ram
43k
The package has been removed from CRAN and BioConductor. Should you even be using it?
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
The barcodes are in location 1-10 and you have the actual list there. I don't know for certain what is in position 11-20 (perhaps spacer, c…
Answer: Including plasmid in transcriptome assemblies
by
GenoMax
141k
> I want to use both STAR and BOWTIE2 for assembly Those programs are aligners not assemblers. But since you are working with bacteria yo…
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
I already have gvcfs called by chromosome and there are 24 gvcfs per sample which I merged them into a single gvcf per sample. Now I want …
Comment: Find subcluster under a cluster, find differential genes in one cluster between
by
bk11
★ 2.3k
First, could you please explain any reason for not using Seurat V5 approach for your data integration mentioned in [here][1]? > Now moving…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
So I'd take the json file located [here][1] and essentially create the whitelist to be all possible combinations of the position 1-10 barco…
Comment: TCGA2STAT Error: Firehose connection
by
Ngrin
• 0
Hey Gnana, could you find a way to solve the issue? I have the same error
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
You simply need to make a list of barcodes one on each line: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-wh…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
GenoMax
141k
> What specifications and operating system would be ideal for my case? For choice of OS: Linux to access the large pool of open source sof…
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