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116,565 results • Page
1 of 2332
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Votes
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0
votes
5
replies
560
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated just now by
Ngrin
• 0 • written 6 months ago by
Gnana
• 0
0
votes
2
replies
20
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
snRNA-seq
STARSolo
scRNA-seq
STAR
just now by
atowns21
• 0
0
votes
0
replies
18
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
37 minutes ago by
alphaflylizard
• 0
2
votes
3
replies
58
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 53 minutes ago by
GenoMax
141k • written 1 hour ago by
Estevão
• 0
0
votes
2
replies
69
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
1 hour ago by
Dylan
• 0
0
votes
1
reply
33
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 1 hour ago by
Pierre Lindenbaum
161k • written 2 hours ago by
Lada
▴ 30
3
votes
10
replies
310
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 hour ago by
Ram
43k • written 17 hours ago by
dominickd
• 0
3
votes
7
replies
336
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 54 minutes ago by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
0
votes
0
replies
28
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 hours ago by
ohtang7
▴ 40
0
votes
0
replies
36
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
3 hours ago by
Kash
▴ 110
2
votes
0
replies
47
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 4 hours ago by
Ram
43k • written 4 hours ago by
carlopecoraro2
★ 2.5k
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
2
votes
2
replies
348
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 5 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
73
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 6 hours ago by
GenoMax
141k • written 6 hours ago by
Srinka
▴ 20
8
votes
5
replies
4.6k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
4
replies
158
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 4 hours ago by
GenoMax
141k • written 6 hours ago by
njornet
▴ 20
5
votes
3
replies
518
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 7 hours ago by
colindaven
6.4k • written 5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
40
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 4 hours ago by
Ram
43k • written 7 hours ago by
SHREYA
• 0
0
votes
3
replies
312
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 7 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
48
views
Merging replicates from Encode project
CHIP-seq
encode
7 hours ago by
Nurken
• 0
1
vote
3
replies
140
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
8 hours ago by
WouterDeCoster
47k
0
votes
3
replies
141
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 6 hours ago by
mchour
• 0 • written 9 hours ago by
rhossen
• 0
1
vote
1
reply
104
views
WGCNA preservation analysis
WGCNA
preservation
updated 8 hours ago by
Michael
54k • written 10 hours ago by
michael.flower.14
▴ 180
0
votes
2
replies
112
views
some error in building kraken2 database
metagenome
kraken2
updated 4 hours ago by
Ram
43k • written 9 hours ago by
Art1ess
• 0
0
votes
1
reply
78
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 hours ago by
bk11
★ 2.3k • written 9 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
83
views
Plots for DNA methylation data
plots
DNA
methylation
updated 7 hours ago by
GenoMax
141k • written 11 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
442
views
python file for coding potential calculator
cpc2.py
updated 11 hours ago by
atharvakarkare14
▴ 10 • written 5 days ago by
Ashok
• 0
1
vote
1
reply
114
views
Failed kmer content
kmer
illumina
ngs
updated 4 hours ago by
Ram
43k • written 12 hours ago by
Kasturi
• 0
0
votes
1
reply
108
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 11 hours ago by
Basti
★ 2.0k • written 13 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
80
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
14 hours ago by
yxwucq
• 0
0
votes
0
replies
64
views
Seurat merge and batch correction
Seurat
15 hours ago by
sooni
▴ 20
0
votes
0
replies
48
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 3 hours ago by
Ram
43k • written 15 hours ago by
SSSJec
• 0
0
votes
5
replies
205
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
updated 19 hours ago by
Pierre Lindenbaum
161k • written 22 hours ago by
Sd
• 0
0
votes
2
replies
135
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
22 hours ago by
sainavyav22
• 0
0
votes
1
reply
105
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 23 hours ago by
Ram
43k • written 23 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
237
views
Error in cnetplot enrichplot package
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
Farhad
• 0
1
vote
4
replies
168
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
79
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
143
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
66
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
125
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
22 hours ago by
dxj294
• 0
0
votes
0
replies
73
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 4 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
110
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 22 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
1
reply
113
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
164
views
from row count to tpm
tpm
row-count
normalization
11 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
73
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
4
replies
173
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
2
votes
3
replies
300
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.8k • written 14 days ago by
javanokendo
▴ 60
0
votes
1
reply
114
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
116,565 results • Page
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Comment: Ideal PC configurations and operating system for bioinformatics laboratory
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
ISCN annotation for SV/CN VCF files
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
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Recent Replies
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…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11"
by
Dylan
• 0
> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Ram
43k
> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
Answer: Difference between samtools "-f 9" and "-f 11"
by
Pierre Lindenbaum
161k
9: read must be paired AND mate must be unmapped 11: read must be paired AND mapped in proper pair AND mate must be unmapped (which is w…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
• 0
could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
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