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699 results • Page 2 of 14
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1
vote
8
replies
254
views
Error with pheatmap - 'from' must be a finite number
pheatmap r deseq2
updated 20 minutes ago by ▴ 20 • written 17 hours ago by • 0
3
votes
8
replies
668
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
21 days ago by Qroid ▴ 40
0
votes
8
replies
575
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 27 days ago by 4.2k • written 29 days ago by ▴ 10
2
votes
8
replies
440
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 16 days ago by 162k • written 16 days ago by ▴ 100
3
votes
8
replies
885
views
Random Access remote BAM files
htslib BAM
updated 5 days ago by • 0 • written 3 months ago by ▴ 20
0
votes
8
replies
565
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 8 days ago by 162k • written 17 days ago by • 0
0
votes
8
replies
527
views
Different output for read length
samtools BAM
18 days ago by marco.barr ▴ 130
1
vote
8
replies
609
views
Downsampling fastq file
downsample fastq
27 days ago by marco.barr ▴ 130
1
vote
8
replies
515
views
Overlapping Ranges within Granges object
Genomicranges IRanges GRanges
updated 10 days ago by 35k • written 14 days ago by ▴ 60
3
votes
8
replies
6.7k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 25 days ago by • 0 • written 5.2 years ago by 11k
3
votes
8
replies
772
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 21 days ago by ▴ 410 • written 25 days ago by ▴ 100
4
votes
7
replies
659
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
28 days ago by e.r.zakiev ▴ 210
1
vote
7
replies
545
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
25 days ago by eebloom ▴ 80
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 17 days ago by • 0 • written 5.8 years ago by ▴ 20
2
votes
7
replies
1.6k
views
Problems when trying to use ensembl-vep
ensembl ensembl-vep docker
updated 8 hours ago by ▴ 400 • written 10 months ago by ▴ 50
3
votes
7
replies
412
views
Z score
Z-score
updated 5 hours ago by 82k • written 5 days ago by ▴ 60
0
votes
7
replies
699
views
Post-imputation plot
michigan-imputation-server quality-control
updated 25 days ago by 3.9k • written 28 days ago by ▴ 10
1
vote
7
replies
606
views
Question regarding WGCNA
WGCNA Network-construction
19 days ago by deepak • 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 10 days ago by ▴ 10 • written 3.7 years ago by ▴ 90
3
votes
7
replies
453
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
28 days ago by Sergio A.S. • 0
8
votes
7
replies
3.9k
views
6 follow
What is the best practice of scRNA workflow for multiple patients and samples using Seurat
scRNA sing-cell RNA seurat integrate
updated 1 day ago by ▴ 640 • written 3.5 years ago by ▴ 70
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 29 days ago by ★ 7.2k • written 9 months ago by ▴ 10
0
votes
7
replies
495
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 15 days ago by ▴ 20 • written 29 days ago by • 0
6
votes
7
replies
443
views
Longest transcript variant per gene
transcript longest variant orthofinder
15 days ago by sansan_96 ▴ 90
4
votes
7
replies
470
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
14 days ago by Chen • 0
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS Bismark DNA-methylation
updated 5 days ago by ★ 2.9k • written 3.9 years ago by ▴ 40
2
votes
7
replies
611
views
KEGG analysis in R
KEGG clusterProfiler Zea-mays
updated 6 days ago by • 0 • written 6 weeks ago by ▴ 90
5
votes
7
replies
567
views
RNA seq analysis
DESeq RNA-seq
13 days ago by Jacek ▴ 20
1
vote
7
replies
660
views
ScRNA data question
scRNA Vlnplot Samples
updated 29 days ago by ★ 2.5k • written 4 weeks ago by ▴ 10
1
vote
7
replies
403
views
samtools write-index
samtools
1 day ago by R.L. • 0
6
votes
6
replies
1.9k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 22 days ago by ▴ 10 • written 2.0 years ago by • 0
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 29 days ago by • 0 • written 5.0 years ago by ▴ 90
2
votes
6
replies
332
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes GATK SNP VCF
5 days ago by anikcropscience ▴ 230
1
vote
6
replies
385
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
7 days ago by Umer ▴ 50
0
votes
6
replies
529
views
How to build ribosomal interval files to use in CollectRnaSeqMetrics for hg38.p14
hg38.p14 ribosomal-intervals
4 hours ago by naaj • 0
4
votes
6
replies
3.9k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 22 days ago by ▴ 30 • written 6.7 years ago by ★ 1.3k
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 20 days ago by ▴ 10 • written 2.6 years ago by • 0
2
votes
6
replies
2.3k
views
Tool: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart annotation Ensembl
updated 1 day ago by ★ 2.0k • written 2.8 years ago by ★ 1.4k
3
votes
6
replies
356
views
Problem in getting geo file through GEOQUERY
geoquery Geo
updated 5 days ago by 44k • written 6 days ago by ▴ 120
4
votes
6
replies
340
views
Error with BiocParallel. No barcodes files found
Barcodes scRNA-seq SingleCellExperiment
4 days ago by bio_info ▴ 20
1
vote
6
replies
449
views
Do I need to go back and filter my long-reads?
alignment nanopore filtering QC ONT
updated 25 days ago by 142k • written 6 weeks ago by ▴ 80
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 9 days ago by ▴ 30 • written 9 months ago by ▴ 870
4
votes
6
replies
12k
views
Looking for differential gene expression between treatment, within a specific cluster (seurat)
seurat
updated 1 day ago by ★ 17k • written 4.7 years ago by ▴ 230
3
votes
6
replies
559
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 15 days ago by ▴ 20 • written 23 days ago by • 0
0
votes
6
replies
532
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 24 days ago by 14k • written 25 days ago by • 0
0
votes
6
replies
295
views
from CRAM to fastq
FASTQ WGS CRAM
updated 5 days ago by 82k • written 6 days ago by • 0
2
votes
6
replies
2.0k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 12 days ago by 44k • written 3.9 years ago by • 0
2
votes
6
replies
445
views
BWA alignment
Samtools bam
updated 13 days ago by ▴ 260 • written 15 days ago by • 0
0
votes
6
replies
2.2k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 19 days ago by 142k • written 3.2 years ago by ▴ 10
2
votes
6
replies
432
views
Harmony integration group.by.var parameter
single-cell harmony
updated 1 day ago by ★ 17k • written 4 days ago by ▴ 640
699 results • Page 2 of 14
Recent Votes
Answer: UMI-Tools knee-method has great influence on the results of white list
Answer: UMI-Tools knee-method has great influence on the results of white list
linkage disequilibrium analysis
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
Answer: linkage disequilibrium analysis
Answer: UMI-Tools knee-method has great influence on the results of white list
A: Fix SAM flags on quality filtered paired-end BAM file
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Recent Replies
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data? by Jack • 0
I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates. Repeats range from polyG tracts around 9-20…
Comment: Best practices in Fungal Genome Assembly by samuel.a.odonnell ▴ 520
For the short-read strains: <br/> I would recommend just using SPADES For the strains with long-reads: <br/> I think spades and masurca as…
Comment: txt file to bigwig by GenoMax 142k
Click on `edit`. That should open the edit window which will have a `Delete` button at bottom right to delete the comment/reply.
Comment: UMI-Tools knee-method has great influence on the results of white list by Assa Yeroslaviz ★ 1.9k
Can you pls make it an answer so that I can accept it? thx
Comment: Best practices in Fungal Genome Assembly by samuel.a.odonnell ▴ 520
I think tools like quickmerge (or Ragtag's patch command) can help for long-read assemblies, but I would definitely avoid using them with s…
Comment: txt file to bigwig by sogand • 0
Hi, I tried to delete my comment but can't see any delete/remove option here! Thanks
Comment: Error with pheatmap - 'from' must be a finite number by Ram 44k
You'd see a different issue if the vector being analyzed contained character entries. This is clearly a problem with NA/NaN/Inf values in t…
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data? by GenoMax 142k
> bacterial genes containing phase variable short sequence repeats in their coding regions Can you describe this in a bit more detail? Are…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by jared.andrews07 ★ 17k
This is exactly my point. You should not have gotten data to this state unintentionally, so you need to double-check what was done upstream…
Comment: Search within posts based on tags using the Biostars API by Ram 44k
Right, that's true. One way to do that would be to get the HTML output of https://www.biostars.org/tag/crispr/ and search it for the first …
Answer: Illumina EPIC v2 IlmnIDs and probe names by Papyrus ★ 2.9k
The ID code and the new features for the EPICv2 are explained in the Illumina documentation which you can access [here][1], in the `Infiniu…
Comment: Error with pheatmap - 'from' must be a finite number by Ram 44k
That answers half of what I asked you. Where's the output to the first command?
Comment: Error with pheatmap - 'from' must be a finite number by Ram 44k
You already have the response to the first one, so there was no need to include that.
Answer: Illumina EPIC v2 IlmnIDs and probe names by GenoMax 142k
The answer is provided in this Bioconductor thread: https://support.bioconductor.org/p/9156675/
Comment: Illumina EPIC v2 IlmnIDs and probe names by rna-seq_researcher ▴ 60
Hi, by any chance did you manage to solve this problem?
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