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1,000 results • Page 5 of 20
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0
votes
0
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192
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RNA-seq: full length gene
RNA-seq
updated 20 days ago by 43k • written 20 days ago by • 0
0
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0
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171
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Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
20 days ago by turcoa1 • 0
0
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0
replies
183
views
Designing single-stable RNA molecules
structure RNA
21 days ago by Edna • 0
0
votes
0
replies
196
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
21 days ago by simplitia ▴ 130
1
vote
1
reply
264
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Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 21 days ago by 82k • written 21 days ago by • 0
0
votes
0
replies
181
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary deeptools correlation
2 days ago by Emily ▴ 20
1
vote
0
replies
192
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How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
21 days ago by rohitsatyam102 ▴ 860
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
21 days ago by synat.keam ▴ 100
0
votes
1
reply
535
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 21 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
176
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
21 days ago by Aspire ▴ 330
0
votes
4
replies
413
views
Highest variable features in single cell data
single-cell
9 days ago by carolofharvest ▴ 40
1
vote
3
replies
448
views
PCA plot
DESeq2 PCAplot
updated 18 days ago by 4.2k • written 22 days ago by ▴ 10
0
votes
0
replies
171
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
22 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
311
views
Annovar using R package
Annovar gnomAD R
21 days ago by DKA ▴ 40
0
votes
5
replies
441
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 21 days ago by 142k • written 22 days ago by ▴ 90
0
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0
replies
168
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 22 days ago by 43k • written 22 days ago by • 0
0
votes
0
replies
329
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
22 days ago by pramach1 ▴ 40
0
votes
1
reply
209
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 22 days ago by • 0 • written 22 days ago by • 0
0
votes
0
replies
168
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
22 days ago by salias • 0
0
votes
5
replies
457
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 19 days ago by 100k • written 22 days ago by ▴ 10
0
votes
0
replies
143
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 22 days ago by 43k • written 22 days ago by • 0
1
vote
2
replies
280
views
alignment result
RNA-seq samtools hisat2
21 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
140
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
23 days ago by Kash ▴ 110
0
votes
1
reply
189
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 22 days ago by ★ 27k • written 23 days ago by • 0
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 22 days ago by 43k • written 23 days ago by ▴ 140
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 23 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
710
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
21 days ago by atowns21 • 0
0
votes
1
reply
213
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 23 days ago by ★ 2.4k • written 23 days ago by • 0
0
votes
0
replies
120
views
The concept of co-occurrence network structure
co-occurence microbiome network
23 days ago by ohtang7 ▴ 40
0
votes
1
reply
209
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated 23 days ago by 142k • written 23 days ago by ▴ 20
0
votes
5
replies
426
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
22 days ago by njornet ▴ 20
0
votes
0
replies
126
views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
129
views
Merging replicates from Encode project
CHIP-seq encode
23 days ago by Nurken • 0
1
vote
3
replies
300
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
23 days ago by WouterDeCoster 47k
1
vote
3
replies
334
views
some error in building kraken2 database
metagenome kraken2
23 days ago by Art1ess • 0
0
votes
1
reply
213
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 23 days ago by ★ 2.4k • written 23 days ago by ▴ 110
1
vote
1
reply
213
views
Failed kmer content
kmer illumina ngs
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy Copy-number-analysis R
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
1
reply
175
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 24 days ago by 43k • written 24 days ago by • 0
0
votes
8
replies
456
views
Error in cnetplot enrichplot package
R
updated 24 days ago by 43k • written 24 days ago by • 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment Genomics Ka-Ks
updated 24 days ago by 43k • written 24 days ago by ▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome gene-family
updated 24 days ago by 43k • written 24 days ago by ▴ 90
0
votes
0
replies
116
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 23 days ago by 43k • written 24 days ago by • 0
0
votes
0
replies
223
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS Meta-analysis
updated 24 days ago by 43k • written 24 days ago by ▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 24 days ago by 10k • written 6.2 years ago by ▴ 10
1
vote
8
replies
539
views
Downsampling fastq file
downsample fastq
16 days ago by marco.barr ▴ 120
0
votes
1
reply
169
views
tbtool
tbtool
updated 24 days ago by 43k • written 24 days ago by • 0
0
votes
10
replies
611
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 16 days ago by 19k • written 24 days ago by • 0
0
votes
1
reply
161
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 24 days ago by 82k • written 24 days ago by • 0
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
24 days ago by manaswwm ▴ 510
1,000 results • Page 5 of 20
Recent Votes
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty by Jordan M Eizenga ▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly by sansan_96 ▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
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