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1,000 results • Page 1 of 20
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Alternative splicing
single-cell suppa rnaseq splicing alternative
just now by newuser2024 • 0
0
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0
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7
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Network Alignment
plugin Cytoscape CytoMCS
26 minutes ago by Akash D ▴ 40
0
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0
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16
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alignment result
samtool RNA-seq analysis hisat2
1 hour ago by ahmad.sajad4541 • 0
0
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0
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23
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Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet hetero Seurat modelHomotypic DoubletFinder
2 hours ago by Jeyong • 0
0
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0
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38
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To get p-values for the TPM
P-value TPM RSEM
3 hours ago by VITALA • 0
0
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0
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43
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PCA plot (Suggestions Needed)
DESeq2 PCAplot
4 hours ago by Aaliya • 0
0
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0
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47
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AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
9 hours ago by Kash ▴ 110
0
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1
reply
79
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How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 5 hours ago by ★ 27k • written 11 hours ago by • 0
0
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2
replies
108
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How to calculate identity percentage between proteins contained in a FASTA file?
percentage FASTA alignment identity
updated 40 minutes ago by ▴ 170 • written 11 hours ago by ▴ 140
2
votes
9
replies
748
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 7 hours ago by 4.2k • written 6 months ago by • 0
0
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10
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312
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
5 hours ago by atowns21 • 0
0
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1
reply
91
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Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 13 hours ago by ★ 2.3k • written 14 hours ago by • 0
0
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1
reply
79
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How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
updated 15 hours ago by 161k • written 15 hours ago by ▴ 30
0
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0
replies
58
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The concept of co-occurrence network structure
co-occurence microbiome network
17 hours ago by ohtang7 ▴ 40
0
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1
reply
105
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Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 19 hours ago by 141k • written 19 hours ago by ▴ 20
0
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4
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196
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Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
updated 17 hours ago by 141k • written 20 hours ago by ▴ 20
0
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0
replies
63
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 17 hours ago by 43k • written 20 hours ago by • 0
0
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0
replies
71
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Merging replicates from Encode project
CHIP-seq encode
21 hours ago by Nurken • 0
1
vote
3
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169
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Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
22 hours ago by WouterDeCoster 47k
0
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3
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192
views
some error in building kraken2 database
metagenome kraken2
7 hours ago by Art1ess • 0
0
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1
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106
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Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 17 hours ago by ★ 2.3k • written 23 hours ago by ▴ 110
1
vote
1
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137
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Failed kmer content
kmer illumina ngs
updated 17 hours ago by 43k • written 1 day ago by • 0
0
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1
reply
170
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Heatmap and rna-seq
RNA-Seq Heatmap and
updated 10 hours ago by 100k • written 1 day ago by ▴ 10
0
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0
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72
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 17 hours ago by 43k • written 1 day ago by • 0
0
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1
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126
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Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 1 day ago by 43k • written 1 day ago by • 0
0
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8
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263
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Error in cnetplot enrichplot package
R
updated 1 day ago by 43k • written 1 day ago by • 0
0
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0
replies
101
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Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 1 day ago by 43k • written 1 day ago by ▴ 200
0
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0
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82
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Analysis of the gene family of a genome.
Genome gene-family
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
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0
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88
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File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 17 hours ago by 43k • written 1 day ago by • 0
0
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0
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131
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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
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3
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2.4k
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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
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225
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Downsampling fastq file
downsample fastq
updated 1 day ago by 43k • written 1 day ago by ▴ 80
0
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1
reply
116
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tbtool
tbtool
updated 1 day ago by 43k • written 1 day ago by • 0
0
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2
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169
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Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 1 day ago by 19k • written 1 day ago by • 0
0
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2
replies
139
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clustalo - align milions of short seq, memory issue
memory clustalo
updated 1 day ago by ★ 27k • written 1 day ago by ▴ 120
0
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1
reply
110
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Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 1 day ago by 82k • written 1 day ago by • 0
0
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0
replies
77
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
1 day ago by manaswwm ▴ 490
0
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0
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67
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Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
21 hours ago by alifafiq1 • 0
0
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0
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77
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How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
1 day ago by feather-W • 0
2
votes
4
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196
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interpretartion of a vcf file
calling genotype ONT variant diploid
32 minutes ago by samuelkalandarov2002 ▴ 10
0
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0
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73
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Annotating single cell data automatically
cell annotation single
1 day ago by Gerard • 0
0
votes
1
reply
134
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RNA-seq bacteria contamination
RNA-seq
updated 1 day ago by 141k • written 1 day ago by • 0
0
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0
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65
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Imputation advice
imputation
1 day ago by kl ▴ 10
0
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0
replies
81
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Trimming best practices for SNP calling
trimming SNP trimmomatic
2 days ago by Enrique • 0
0
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0
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68
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Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
2 days ago by sativus ▴ 20
0
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0
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74
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Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
2 days ago by Biostars2200 • 0
0
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0
replies
108
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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
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5
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414
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Marking duplicates using UMIs
Deduplication UMI
updated 1 day ago by 19k • written 3 days ago by • 0
0
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0
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134
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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
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0
replies
136
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Bacterial genome alignment with mauve
Bacteria mauve genome
3 days ago by rthapa ▴ 90
1,000 results • Page 1 of 20
Recent Votes
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Read pair orientation : Illumina TruSeq Stranded mRNA library
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
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Recent Replies
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
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…
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