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1,000 results • Page 6 of 20
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0
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0
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97
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Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
23 days ago by alifafiq1 • 0
0
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0
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102
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
24 days ago by feather-W • 0
2
votes
4
replies
377
views
interpretartion of a vcf file
calling genotype ONT variant diploid
22 days ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
99
views
Annotating single cell data automatically
cell annotation single
24 days ago by Gerard • 0
0
votes
1
reply
200
views
RNA-seq bacteria contamination
RNA-seq
updated 24 days ago by 142k • written 24 days ago by • 0
0
votes
0
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96
views
Imputation advice
imputation
24 days ago by kl ▴ 10
0
votes
0
replies
117
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
24 days ago by Enrique • 0
0
votes
0
replies
92
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
24 days ago by sativus ▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
24 days ago by Biostars2200 • 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 24 days ago by 8.7k • written 24 days ago by • 0
2
votes
5
replies
535
views
Marking duplicates using UMIs
Deduplication UMI
updated 24 days ago by 19k • written 26 days ago by • 0
0
votes
0
replies
157
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 25 days ago by 43k • written 26 days ago by • 0
0
votes
0
replies
161
views
Bacterial genome alignment with mauve
Bacteria mauve genome
26 days ago by rthapa ▴ 90
0
votes
0
replies
156
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
26 days ago by Mamatha Y S • 0
0
votes
2
replies
320
views
bam merging for archaic samples
samtools bam
updated 25 days ago by 43k • written 26 days ago by ▴ 100
1
vote
0
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561
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
26 days ago by mathavanbioinfo ▴ 90
2
votes
5
replies
785
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 26 days ago by ▴ 770 • written 27 days ago by ★ 2.4k
0
votes
0
replies
209
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 27 days ago by 43k • written 27 days ago by • 0
0
votes
0
replies
207
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
27 days ago by Nitin • 0
0
votes
0
replies
201
views
Chemical structure validation
structure cap validation metabolite
27 days ago by Rodolfo Adrián • 0
0
votes
1
reply
303
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 27 days ago by 142k • written 27 days ago by ▴ 10
0
votes
0
replies
232
views
Copy number variation plot
Copy-number-variation genomics
updated 27 days ago by 43k • written 27 days ago by • 0
0
votes
0
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209
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
27 days ago by DanielEB_fisk ▴ 20
0
votes
1
reply
323
views
Could you please assist in identifying this cluster?
single-cell
updated 27 days ago by 43k • written 27 days ago by ▴ 40
0
votes
0
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225
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 27 days ago by 43k • written 27 days ago by • 0
0
votes
0
replies
215
views
miRDeep2: How to get the read counts
mirdeep2
27 days ago by Atul K. • 0
0
votes
0
replies
219
views
Lncipedia GTF file error
Proteomics
updated 27 days ago by 43k • written 27 days ago by ▴ 30
3
votes
3
replies
551
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 26 days ago by 14k • written 27 days ago by ▴ 580
0
votes
2
replies
594
views
How to get the reference panel for UKBB
UKBB GWAS clump
28 days ago by 航太郎 • 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 28 days ago by 142k • written 28 days ago by • 0
0
votes
2
replies
420
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
28 days ago by Ashok • 0
0
votes
2
replies
462
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
27 days ago by Ashok • 0
0
votes
0
replies
231
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 28 days ago by 43k • written 28 days ago by ▴ 10
0
votes
2
replies
471
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
27 days ago by _quantum_girl_ ▴ 10
0
votes
0
replies
231
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
24 days ago by Javier • 0
0
votes
0
replies
211
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
28 days ago by enferdeflame • 0
1
vote
1
reply
453
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 26 days ago by ★ 7.2k • written 28 days ago by ▴ 280
0
votes
1
reply
417
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 28 days ago by 43k • written 20 months ago by • 0
0
votes
0
replies
175
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 28 days ago by 43k • written 28 days ago by ▴ 10
0
votes
0
replies
196
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
28 days ago by P. • 0
0
votes
0
replies
186
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
28 days ago by ekirsch • 0
1
vote
1
reply
522
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
27 days ago by renan.igor • 0
0
votes
0
replies
214
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
29 days ago by synat.keam ▴ 100
0
votes
1
reply
306
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 29 days ago by 142k • written 29 days ago by • 0
0
votes
4
replies
655
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
27 days ago by Kai Xin • 0
1
vote
1
reply
255
views
Retrieve a % coverage for each transcript
RNA-seq
updated 29 days ago by 43k • written 29 days ago by ▴ 40
0
votes
2
replies
427
views
How can I solve this error?
metal
29 days ago by 22211020193 • 0
0
votes
0
replies
187
views
Struggling to lift genome builds
PLINK liftover GWAS
updated 29 days ago by 142k • written 29 days ago by • 0
1
vote
4
replies
412
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 142k • written 29 days ago by • 0
0
votes
0
replies
374
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
29 days ago by Ronin • 0
1,000 results • Page 6 of 20
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Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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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?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
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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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