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1,000 results • Page 5 of 20
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4
votes
7
replies
645
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 6 weeks ago by ★ 3.8k • written 6 weeks ago by ▴ 140
3
votes
7
replies
1.4k
views
Find 3'UTRs for species
Assembly alignment
updated 11 months ago by 43k • written 4.7 years ago by ▴ 110
0
votes
7
replies
583
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 43k • written 3 months ago by ▴ 100
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by • 0 • written 3.5 years ago by • 0
1
vote
7
replies
833
views
What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 43k • written 10 months ago by ▴ 70
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
0
votes
7
replies
403
views
single nuclei sequencing questions
fastq single-nuclei-sequencing
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 3 months ago by 43k • written 21 months ago by ▴ 10
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST R
updated 3 months ago by ▴ 140 • written 2.8 years ago by ▴ 20
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
4
votes
7
replies
632
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by ▴ 20
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 10 months ago by 43k • written 12 months ago by ▴ 80
7
votes
7
replies
620
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
1
vote
7
replies
1.6k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq alignment Bowtie2 STAR
updated 10 months ago by 142k • written 10 months ago by ▴ 60
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean error
updated 8 months ago by 142k • written 8 months ago by • 0
6
votes
7
replies
600
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 11 months ago by 4.2k • written 11 months ago by ▴ 40
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 43k • written 8.1 years ago by ▴ 330
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr fold-change
updated 8 months ago by 43k • written 5.9 years ago by ▴ 80
3
votes
7
replies
1.1k
views
IGV not showing bigwig track information
bigwig IGV ChIP-seq
updated 6 months ago by 82k • written 6 months ago by ▴ 10
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe vg
updated 10 months ago by ▴ 460 • written 10 months ago by • 0
0
votes
7
replies
474
views
Error "ckalloc: request for negative space" about multiz
multiz
10 weeks ago by marh32 • 0
4
votes
7
replies
793
views
Alternative for grep in a for loop
linux
updated 7 months ago by 43k • written 7 months ago by ▴ 20
1
vote
7
replies
844
views
alignment tool for big data
sequence
updated 11 months ago by 43k • written 4.6 years ago by ▴ 20
5
votes
7
replies
974
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 12 months ago by • 0 • written 4.4 years ago by ▴ 50
0
votes
7
replies
1.1k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 10 months ago by 43k • written 5.2 years ago by • 0
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.2 years ago by ▴ 70
5
votes
7
replies
483
views
RNA seq analysis
DESeq RNA-seq
1 day ago by Jacek ▴ 20
0
votes
7
replies
475
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 400 • written 3 months ago by ▴ 210
1
vote
7
replies
536
views
Question regarding WGCNA
WGCNA Network-construction
7 days ago by deepak • 0
3
votes
7
replies
542
views
How does kallisto handle multi mapped reads?
kallisto
updated 12 weeks ago by ★ 6.0k • written 12 weeks ago by ▴ 150
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
0
votes
7
replies
2.0k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix CIBERSORTx signature
updated 6 months ago by • 0 • written 22 months ago by • 0
0
votes
7
replies
786
views
Search for specific SNPs in VCF files of patients.
ANNOVAR vcftools bcftools GATK VCF
updated 4 months ago by 43k • written 4 months ago by ▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 5 weeks ago by 43k • written 3.7 years ago by ▴ 20
0
votes
7
replies
937
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.5 years ago by ▴ 160
2
votes
7
replies
1.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency gnomad annovar
updated 7 months ago by 43k • written 7 months ago by • 0
2
votes
7
replies
672
views
Maker: Combining Annotations for Large Genomes
Maker Genome annotation
3 months ago by Kinoppy • 0
1
vote
7
replies
919
views
help with weird PCA? (vcfR)
vcftools vcfR R
6 months ago by MaeBH • 0
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 11 months ago by 43k • written 5.5 years ago by ★ 2.6k
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
0
votes
7
replies
467
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 7 weeks ago by 142k • written 7 weeks ago by • 0
4
votes
7
replies
843
views
SNP IDs
SNP
6 months ago by kl ▴ 10
1
vote
7
replies
1.9k
views
for loop in a bash script
bash
updated 10 months ago by 43k • written 2.6 years ago by • 0
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
1
vote
7
replies
1.9k
views
Filtering a VCF by "IMP" flag in INFO with bcftools
vcf bcftools
updated 11 months ago by 43k • written 19 months ago by ▴ 40
0
votes
7
replies
457
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 5 weeks ago by ★ 2.9k • written 6 weeks ago by ▴ 10
2
votes
7
replies
589
views
Need a link to OLDERADO server
pdb protein nmr structure
9 weeks ago by b2003 • 0
0
votes
7
replies
625
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
11 weeks ago by sacryt • 0
1,000 results • Page 5 of 20
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Recent Replies
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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…
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