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1,000 results • Page 5 of 20
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2
votes
7
replies
889
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional scRNAseq
9 months ago by cwwong13 ▴ 40
1
vote
7
replies
839
views
What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 44k • written 10 months ago by ▴ 70
0
votes
7
replies
2.3k
views
Command not found after pip install spliceai
software error
updated 7 months ago by • 0 • written 3.6 years ago by • 0
2
votes
7
replies
974
views
Removing duplicates
duplicates ONT minimap2
updated 4 weeks ago by ▴ 580 • written 4 weeks ago by • 0
0
votes
7
replies
745
views
error MarkerScanner.pl
amphora2
updated 5 months ago by 44k • written 5 months ago by • 0
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 4 weeks ago by 44k • written 7.7 years ago by ▴ 70
3
votes
7
replies
3.3k
views
vcf filter for FORMAT argument (DP/GQ/GQX > 30) multiple (380) vcf file
vcffilter vcftools sequencing
updated 11 months ago by 44k • written 4.2 years ago by ▴ 10
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
484
views
Error "ckalloc: request for negative space" about multiz
multiz
11 weeks ago by marh32 • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 6 weeks ago by 44k • written 3.8 years ago by ▴ 20
0
votes
7
replies
599
views
Iterate through Seurat object to add patient information
R Seurat
updated 3 months ago by 44k • written 3 months ago by ▴ 100
5
votes
7
replies
877
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 280
0
votes
7
replies
472
views
DESeq: too low p-value for RNAseq
R DESeq p-value RNA-seq FDR
updated 6 weeks ago by ★ 2.9k • written 6 weeks ago by ▴ 10
2
votes
7
replies
544
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
3 months ago by oasiswho • 0
4
votes
7
replies
799
views
Alternative for grep in a for loop
linux
updated 7 months ago by 44k • written 7 months ago by ▴ 20
0
votes
7
replies
481
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 7 weeks ago by 142k • written 7 weeks ago by • 0
6
votes
7
replies
613
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
1
vote
7
replies
1.6k
views
Typical percentage of multimapping reads in human rna-seq?
RNA-seq alignment Bowtie2 STAR
updated 11 months ago by 142k • written 11 months ago by ▴ 60
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
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 44k • written 5.5 years ago by ★ 2.6k
0
votes
7
replies
494
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 410 • written 3 months ago by ▴ 210
0
votes
7
replies
4.5k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq alignment software-error next-gen sequence
updated 5 months ago by 44k • written 6.0 years ago by • 0
4
votes
7
replies
2.3k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 3 months ago by 44k • written 22 months ago by ▴ 10
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 44k • written 8.1 years ago by ▴ 330
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R heatmap
updated 7 months ago by 88k • written 5.5 years ago by ▴ 30
4
votes
7
replies
851
views
SNP IDs
SNP
6 months ago by kl ▴ 10
3
votes
7
replies
431
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
22 days ago by Sergio A.S. • 0
1
vote
7
replies
960
views
Filtering a 10X generated .bam file based on a list of barcodes
snRNA-seq scRNA-seq samtools BAM RNA-seq
7 months ago by jhnicolas • 0
4
votes
7
replies
648
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 5 weeks ago by 44k • written 5 weeks ago by ▴ 20
0
votes
7
replies
635
views
Trying to extract .cram file read sequences into array
CRAM pysam reads samtools
12 weeks ago by sacryt • 0
3
votes
7
replies
1.5k
views
Find 3'UTRs for species
Assembly alignment
updated 11 months ago by 44k • written 4.8 years ago by ▴ 110
1
vote
7
replies
585
views
Question regarding WGCNA
WGCNA Network-construction
12 days ago by deepak • 0
2
votes
7
replies
725
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq contamination
updated 9 weeks ago by ▴ 410 • written 10 weeks ago by ▴ 20
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 12 months ago by ▴ 40
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 11 months ago by 44k • written 8.1 years ago by ▴ 50
0
votes
7
replies
1.1k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 11 months ago by 44k • written 5.2 years ago by • 0
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 44k • written 4.9 years ago by ▴ 120
2
votes
7
replies
1.4k
views
VG mapping paired-end reads: error [xg]: multiple hits for XXX
variation-graph reads pangenome vg paired-end
8 months ago by nkls063408 • 0
0
votes
7
replies
2.7k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 9 months ago by • 0 • written 2.7 years ago by ▴ 100
0
votes
7
replies
672
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 6 months ago by 161k • written 6 months ago by • 0
3
votes
7
replies
536
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
10 weeks ago by Fadlilah ▴ 10
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 6 months ago by • 0 • written 16 months ago by ▴ 30
1
vote
7
replies
887
views
Ribosomal cluster
seurat single-cell
7 months ago by Chris ▴ 280
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
4
votes
7
replies
661
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 7 weeks ago by ★ 3.8k • written 7 weeks ago by ▴ 140
2
votes
7
replies
684
views
Maker: Combining Annotations for Large Genomes
Maker Genome annotation
3 months ago by Kinoppy • 0
0
votes
7
replies
942
views
Mugsy error -directory must be a directory
Mugsy
updated 8 months ago by 44k • written 3.5 years ago by ▴ 160
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 11 months ago by 44k • written 6.8 years ago by ▴ 70
5
votes
7
replies
993
views
Salmon index not progressing
salmon
updated 8 months ago by 54k • written 8 months ago by ▴ 160
1,000 results • Page 5 of 20
Recent Votes
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
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Recent Replies
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY by ATpoint 82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY by ATpoint 82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by ezz3 • 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix by andersdetermig ▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by Pierre Lindenbaum 161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot by Ghada • 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by LChart 3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY by bk11 ★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by Dave Carlson ★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
I want to get lot of files through code
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