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45 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
8
votes
5
replies
4.7k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 42 minutes ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
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
0
votes
6
replies
575
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 3 minutes ago by
Ram
43k • written 6 months ago by
Gnana
• 0
1
vote
5
replies
567
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 1 hour ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
5
votes
3
replies
520
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
3
replies
443
views
python file for coding potential calculator
cpc2.py
updated 12 hours ago by
atharvakarkare14
▴ 10 • written 5 days ago by
Ashok
• 0
3
votes
7
replies
357
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 1 hour ago by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
2
votes
2
replies
351
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 6 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
3
votes
10
replies
328
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 2 hours ago by
Ram
43k • written 18 hours ago by
dominickd
• 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
1
vote
5
replies
271
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
4 hours ago by
anasjamshed
▴ 120
0
votes
8
replies
238
views
Error in cnetplot enrichplot package
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
Farhad
• 0
0
votes
6
replies
211
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
27 minutes ago by
Sd
• 0
1
vote
3
replies
194
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
updated 5 hours ago by
ATpoint
81k • written 1 day ago by
HyperEvo
• 0
2
votes
3
replies
176
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 10 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
2
votes
3
replies
166
views
from row count to tpm
tpm
row-count
normalization
12 hours ago by
michelafrancesconi9
▴ 20
0
votes
4
replies
162
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 5 hours ago by
GenoMax
141k • written 7 hours ago by
njornet
▴ 20
0
votes
3
replies
145
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
3
replies
143
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
9 hours ago by
WouterDeCoster
47k
0
votes
2
replies
136
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
23 hours ago by
sainavyav22
• 0
0
votes
2
replies
125
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
23 hours ago by
dxj294
• 0
0
votes
2
replies
117
views
some error in building kraken2 database
metagenome
kraken2
updated 4 hours ago by
Ram
43k • written 10 hours ago by
Art1ess
• 0
1
vote
1
reply
114
views
Failed kmer content
kmer
illumina
ngs
updated 4 hours ago by
Ram
43k • written 13 hours ago by
Kasturi
• 0
0
votes
1
reply
109
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 11 hours ago by
Basti
★ 2.0k • written 14 hours ago by
qudrat.nii
▴ 10
1
vote
1
reply
108
views
WGCNA preservation analysis
WGCNA
preservation
updated 9 hours ago by
Michael
54k • written 11 hours ago by
michael.flower.14
▴ 180
0
votes
1
reply
84
views
Plots for DNA methylation data
plots
DNA
methylation
updated 8 hours ago by
GenoMax
141k • written 11 hours ago by
sarahawan92
▴ 10
0
votes
2
replies
82
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
2 hours ago by
Dylan
• 0
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
15 hours ago by
yxwucq
• 0
0
votes
1
reply
80
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 4 hours ago by
bk11
★ 2.3k • written 10 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
76
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
0
votes
0
replies
74
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
2
votes
3
replies
72
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
Estevão
• 0
0
votes
0
replies
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
8 hours ago by
alifafiq1
• 0
0
votes
0
replies
64
views
Seurat merge and batch correction
Seurat
16 hours ago by
sooni
▴ 20
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 4 hours ago by
Ram
43k • written 16 hours ago by
SSSJec
• 0
2
votes
0
replies
49
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 4 hours ago by
Ram
43k • written 5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
48
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 2 hours ago by
Pierre Lindenbaum
161k • written 3 hours ago by
Lada
▴ 30
0
votes
0
replies
49
views
Merging replicates from Encode project
CHIP-seq
encode
8 hours ago by
Nurken
• 0
0
votes
3
replies
42
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
snRNA-seq
STARSolo
scRNA-seq
STAR
updated just now by
GenoMax
141k • written 1 hour ago by
atowns21
• 0
0
votes
0
replies
41
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
0
replies
39
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
4 hours ago by
Kash
▴ 110
0
votes
0
replies
32
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
4 hours ago by
ohtang7
▴ 40
0
votes
1
reply
30
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 42 minutes ago by
bk11
★ 2.3k • written 1 hour ago by
alphaflylizard
• 0
0
votes
1
reply
12
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 11 minutes ago by
GenoMax
141k • written 18 minutes ago by
heelpPlease
• 0
45 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: 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
Not as far as I see. 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-…
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…
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
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