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25
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3.7k
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Forum: Site Use Guidelines
meta biostars Guidelines
updated 1 hour ago by 43k • written 14.6 years ago by 100k
3
votes
10
replies
331
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 3 hours ago by 43k • written 19 hours ago by • 0
0
votes
8
replies
239
views
Error in cnetplot enrichplot package
R
updated 23 hours ago by 43k • written 1 day ago by • 0
3
votes
7
replies
370
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 2 hours ago by ★ 2.3k • written 6 weeks ago by • 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
6
replies
64
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
snRNA-seq STARSolo scRNA-seq STAR
14 minutes ago by atowns21 • 0
0
votes
6
replies
582
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 44 minutes ago by 43k • written 6 months ago by • 0
1
vote
5
replies
271
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
5 hours ago by anasjamshed ▴ 120
8
votes
5
replies
4.7k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by ▴ 60
1
vote
5
replies
568
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 2 hours ago by • 0 • written 3 months ago by • 0
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 141k • written 7 hours ago by ▴ 20
2
votes
3
replies
82
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 hours ago by 141k • written 2 hours ago by • 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 23 hours ago by 10k • written 6.1 years ago by ▴ 10
2
votes
3
replies
176
views
interpretartion of a vcf file
calling genotype ONT variant diploid
updated 11 hours ago by 161k • written 1 day ago by ▴ 10
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
2
votes
3
replies
167
views
from row count to tpm
tpm row-count normalization
12 hours ago by michelafrancesconi9 ▴ 20
0
votes
3
replies
313
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 8 hours ago by 6.4k • written 8 days ago by • 0
5
votes
3
replies
521
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
updated 8 hours ago by 6.4k • written 5 days ago by ▴ 40
0
votes
3
replies
145
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 7 hours ago by • 0 • written 10 hours ago by • 0
0
votes
3
replies
443
views
python file for coding potential calculator
cpc2.py
updated 12 hours ago by ▴ 10 • written 5 days ago by • 0
1
vote
3
replies
195
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
updated 6 hours ago by 81k • written 1 day ago by • 0
0
votes
2
replies
117
views
some error in building kraken2 database
metagenome kraken2
updated 5 hours ago by 43k • written 10 hours ago by • 0
2
votes
2
replies
352
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 6 hours ago by 161k • written 8 months ago by ▴ 80
0
votes
2
replies
95
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
2 hours ago by Dylan • 0
1
vote
1
reply
115
views
Failed kmer content
kmer illumina ngs
updated 5 hours ago by 43k • written 14 hours ago by • 0
0
votes
1
reply
109
views
Heatmap and rna-seq
RNA-Seq Heatmap and
updated 12 hours ago by ★ 2.0k • written 15 hours ago by ▴ 10
1
vote
1
reply
108
views
WGCNA preservation analysis
WGCNA preservation
updated 10 hours ago by 54k • written 12 hours ago by ▴ 180
0
votes
1
reply
84
views
Plots for DNA methylation data
plots DNA methylation
updated 9 hours ago by 141k • written 12 hours ago by ▴ 10
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 141k • written 7 hours ago by ▴ 20
0
votes
1
reply
80
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 5 hours ago by ★ 2.3k • written 11 hours ago by ▴ 110
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 161k • written 3 hours ago by ▴ 30
0
votes
1
reply
34
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 1 hour ago by ★ 2.3k • written 2 hours ago by • 0
1
vote
1
reply
26
views
Including plasmid in transcriptome assemblies
Bacteria BOWTIE2 Transcriptomics STAR
updated 55 minutes ago by 141k • written 1 hour ago by • 0
0
votes
1
reply
69
views
Seurat merge and batch correction
Seurat
updated just now by 43k • written 16 hours ago by ▴ 20
2
votes
0
replies
52
views
News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 5 hours ago by 43k • written 6 hours ago by ★ 2.5k
0
votes
0
replies
74
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 5 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
42
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 5 hours ago by 43k • written 8 hours ago by • 0
1
vote
0
replies
14
views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
26 minutes ago by Biostar 2.7k
0
votes
0
replies
50
views
Merging replicates from Encode project
CHIP-seq encode
9 hours ago by Nurken • 0
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
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
9 hours ago by alifafiq1 • 0
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
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 43k • written 16 hours ago by • 0
0
votes
0
replies
34
views
The concept of co-occurrence network structure
co-occurence microbiome network
5 hours ago by ohtang7 ▴ 40
44 results • Page 1 of 1
Recent Votes
C: Threshold over percentage identity in blastn
A: Threshold over percentage identity in blastn
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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Great Question to Ann ★ 2.4k
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Recent Replies
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- library(Seurat) …
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…
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…
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