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1,000 results • Page 1 of 20
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0
votes
0
replies
14
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet hetero Seurat modelHomotypic DoubletFinder
1 hour ago by Jeyong • 0
0
votes
0
replies
19
views
To get p-values for the TPM
P-value TPM RSEM
1 hour ago by VITALA • 0
0
votes
0
replies
34
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
3 hours ago by Aaliya • 0
0
votes
0
replies
44
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
8 hours ago by Kash ▴ 110
0
votes
1
reply
70
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 3 hours ago by ★ 27k • written 9 hours ago by • 0
0
votes
1
reply
89
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage FASTA alignment identity
updated 9 hours ago by 141k • written 10 hours ago by ▴ 140
2
votes
9
replies
741
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 6 hours ago by 4.2k • written 6 months ago by • 0
0
votes
10
replies
303
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
4 hours ago by atowns21 • 0
0
votes
1
reply
89
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 12 hours ago by ★ 2.3k • written 12 hours ago by • 0
0
votes
1
reply
76
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
updated 14 hours ago by 161k • written 14 hours ago by ▴ 30
0
votes
0
replies
55
views
The concept of co-occurrence network structure
co-occurence microbiome network
16 hours ago by ohtang7 ▴ 40
0
votes
1
reply
103
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 18 hours ago by 141k • written 18 hours ago by ▴ 20
0
votes
4
replies
194
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
updated 16 hours ago by 141k • written 18 hours ago by ▴ 20
0
votes
0
replies
61
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 16 hours ago by 43k • written 19 hours ago by • 0
0
votes
0
replies
68
views
Merging replicates from Encode project
CHIP-seq encode
19 hours ago by Nurken • 0
1
vote
3
replies
167
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
20 hours ago by WouterDeCoster 47k
0
votes
3
replies
184
views
some error in building kraken2 database
metagenome kraken2
6 hours ago by Art1ess • 0
0
votes
1
reply
104
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 16 hours ago by ★ 2.3k • written 22 hours ago by ▴ 110
1
vote
1
reply
134
views
Failed kmer content
kmer illumina ngs
updated 16 hours ago by 43k • written 1 day ago by • 0
0
votes
1
reply
168
views
Heatmap and rna-seq
RNA-Seq Heatmap and
updated 9 hours ago by 100k • written 1 day ago by ▴ 10
0
votes
0
replies
69
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 15 hours ago by 43k • written 1 day ago by • 0
0
votes
1
reply
124
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
8
replies
261
views
Error in cnetplot enrichplot package
R
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
99
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 1 day ago by 43k • written 1 day ago by ▴ 200
0
votes
0
replies
81
views
Analysis of the gene family of a genome.
Genome gene-family
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
votes
0
replies
87
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 16 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
131
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 43k • written 1 day ago by ▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 1 day ago by 10k • written 6.1 years ago by ▴ 10
1
vote
5
replies
224
views
Downsampling fastq file
downsample fastq
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
votes
1
reply
116
views
tbtool
tbtool
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
2
replies
169
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 19k • written 1 day ago by • 0
0
votes
2
replies
139
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 1 day ago by ★ 27k • written 1 day ago by ▴ 120
0
votes
1
reply
110
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 1 day ago by 82k • written 1 day ago by • 0
0
votes
0
replies
77
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
1 day ago by manaswwm ▴ 490
0
votes
0
replies
66
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
20 hours ago by alifafiq1 • 0
0
votes
0
replies
77
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
1 day ago by feather-W • 0
2
votes
3
replies
187
views
interpretartion of a vcf file
calling genotype ONT variant diploid
updated 21 hours ago by 161k • written 1 day ago by ▴ 10
0
votes
0
replies
73
views
Annotating single cell data automatically
cell annotation single
1 day ago by Gerard • 0
0
votes
1
reply
134
views
RNA-seq bacteria contamination
RNA-seq
updated 1 day ago by 141k • written 1 day ago by • 0
0
votes
0
replies
65
views
Imputation advice
imputation
1 day ago by kl ▴ 10
0
votes
0
replies
81
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
1 day ago by Enrique • 0
0
votes
0
replies
68
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
1 day ago by sativus ▴ 20
0
votes
0
replies
73
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
1 day ago by Biostars2200 • 0
0
votes
0
replies
105
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by 8.7k • written 2 days ago by • 0
2
votes
5
replies
413
views
Marking duplicates using UMIs
Deduplication UMI
updated 1 day ago by 19k • written 3 days ago by • 0
0
votes
0
replies
134
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria mauve genome
3 days ago by rthapa ▴ 90
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
3 days ago by Mamatha Y S • 0
0
votes
2
replies
243
views
bam merging for archaic samples
samtools bam
updated 2 days ago by 43k • written 3 days ago by ▴ 100
1
vote
0
replies
533
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
4 days ago by mathavanbioinfo ▴ 90
1,000 results • Page 1 of 20
Recent Votes
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Interested in Spatial Omics?
Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Recent Replies
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 390
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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