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121,926 results • Page 89 of 2439
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505
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Transposable detections for long reads
transposable-elements tetyper
updated 14 months ago by 153k • written 14 months ago by • 0
0
votes
0
replies
437
views
parseCSQToGRanges in VariantAnnotation
bioconductor
14 months ago by ramiro.barrantes ▴ 60
1
vote
1
reply
857
views
Data Table for MONDO, DOID, UBERON and Cell Ontology
Ontology DOID Cell MONDO UBERON
updated 14 months ago by 166k • written 14 months ago by ★ 9.6k
0
votes
0
replies
406
views
How do I infer the proportion of aneuploid cells using sequencing data?
purecn copynumber next-gen cnvkit wgs
14 months ago by Actinidia • 0
0
votes
0
replies
417
views
GATK BwaSpark parameter optimisation
parallel-computing gatk bwaspark
updated 14 months ago by 45k • written 14 months ago by ▴ 20
1
vote
4
replies
904
views
Doubt regarding Nanomolar calculation for dsDNA
Illumina Nanomolar
14 months ago by alenew.am ▴ 10
1
vote
2
replies
846
views
how to perform the GSEA for multi groups
GSEA
14 months ago by alwayshope ▴ 40
2
votes
2
replies
817
views
kb count -x parameter - what are the three parts?
kb_python umi cell-barcodes kallisto
updated 14 months ago by ★ 1.9k • written 14 months ago by ▴ 80
0
votes
5
replies
1.0k
views
Suggestions for resource for running R training
R environments training
updated 14 months ago by ★ 2.1k • written 14 months ago by ▴ 820
0
votes
2
replies
699
views
Small RNA Seq Data-Removing Adapters- Illumina GA2 instrument
Sequencing
14 months ago by jspe • 0
0
votes
1
reply
636
views
computeMatrix on 2 regions with replicates
deepTools ChIP-Seq computeMatrix
updated 14 months ago by ★ 1.6k • written 14 months ago by ▴ 10
0
votes
0
replies
347
views
Can I use CEMiTool to analyze single cell RNA seq data?
CEMiTool single-cell
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
2
replies
967
views
Filter our reads from multiple hosts
genome metagenome virus host
14 months ago by Luca Arbore ▴ 10
0
votes
0
replies
445
views
Issue with AMR gene identification using tools like CARD (RGI), abricate, Patric, ariba, amrfinderplus.
resistant-gene
updated 14 months ago by 45k • written 14 months ago by ▴ 110
1
vote
2
replies
674
views
which data type I can use to bulid machine learning.
Machine-learning FPKM log2foldchange
14 months ago by Qiang ▴ 10
0
votes
0
replies
452
views
Accessing PubMed Central full-texts via FTP?
PMCID epmc_ftxt pmc europepmc
14 months ago by jeremy.clark • 0
0
votes
0
replies
424
views
Navigating Haplotype-Based Association Studies: Software Recommendations and Conversion Challenges
gcta shapeit gwas haplotype phasing
14 months ago by PKW ▴ 110
0
votes
1
reply
951
views
issue with kneaddata
contamination kneaddata
updated 14 months ago by 153k • written 14 months ago by • 0
0
votes
0
replies
380
views
activepathways background list problem
integration atacseq rnaseq activepathways
14 months ago by biology_inform ▴ 60
1
vote
2
replies
948
views
snpEff database build: FATAL ERROR: No CDS checked
gtf snpEff CDS
14 months ago by rwherman13 • 0
0
votes
1
reply
1.1k
views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated 14 months ago by 89k • written 14 months ago by ▴ 420
4
votes
2
replies
845
views
conda R environment warnings - error
R conda
updated 14 months ago by 89k • written 14 months ago by ▴ 180
0
votes
1
reply
793
views
Difference between samtools stats insert size and TLEN in SAM/BAM file.
samtools insert-size SAM
updated 14 months ago by 45k • written 14 months ago by • 0
11
votes
11
replies
2.2k
views
Can't increase font size for x axis
R ggplot2
14 months ago by Chris ▴ 360
0
votes
0
replies
504
views
Orientation bias in Mutect2 variant calling
mutect variant-calling
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
1
reply
920
views
Is it possible to index VCF files and merged the CNVs therein contained using VCF files created from exome sequencing data
variant-calling
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
2
replies
653
views
How to find the mapping file for converting Illumina reports SNPid to rsid for build 28 ?
illumina
14 months ago by vasank1958 • 0
1
vote
0
replies
495
views
Predicting ddG stability of multi-mutation protein variants
ddG protein-stability
updated 14 months ago by 45k • written 14 months ago by ★ 1.5k
1
vote
4
replies
884
views
Make the normalized counts from treatment relative to control-EdgeR
normalized-counts EdgeR
updated 14 months ago by 45k • written 14 months ago by • 0
3
votes
2
replies
1.1k
views
How to Specify genome version (GRCh37 release 104) in VEP REST API?
VEP
updated 14 months ago by 45k • written 14 months ago by ▴ 20
1
vote
4
replies
1.2k
views
Missense variant proteins 3D Structure prediction
model protein-structure alphafold
14 months ago by Esraa ▴ 10
1
vote
2
replies
673
views
Can I analyze single-end and paired-end RNA-Seq data together?
RNA-Seq
updated 14 months ago by ▴ 130 • written 14 months ago by ▴ 10
0
votes
1
reply
534
views
T cell subtype annotation
seurat single-cell SingleCellExperiment
updated 10 months ago by ▴ 40 • written 14 months ago by • 0
0
votes
0
replies
526
views
Job: PhD positions for autoimmune disease at UKSH/Uni Luebeck
PhD autoimmune-disease
updated 14 months ago by 45k • written 14 months ago by ▴ 40
3
votes
14
replies
2.6k
views
vg installation on MacOS failing: "ld: -headerpad: not a hexadecimal number: -headerpad_max_install_names"
macos vg
updated 14 months ago by 153k • written 14 months ago by ▴ 10
0
votes
6
replies
2.2k
views
SPADES Result Comparison
illumina genome SPAdes assembly
14 months ago by SomeOne ▴ 240
0
votes
0
replies
465
views
How to Obtain a GMT File for Pathway Enrichment Analysis in Gallus gallus Metabolomics Data?
metabolomics gsea pathways gmt
14 months ago by DareDevil ★ 4.4k
0
votes
0
replies
535
views
mismatch allele problem PLINK
PLINK
updated 14 months ago by 45k • written 14 months ago by • 0
0
votes
0
replies
420
views
RepeatMasker. Repeat identification.
RepeatMasker
14 months ago by Николай • 0
0
votes
0
replies
547
views
News: Online course: Metabolomics with R/Bioconductor (5th edition)
Metabolomics Bioconductor R
updated 14 months ago by 45k • written 14 months ago by ★ 2.6k
2
votes
1
reply
667
views
I am getting an error with Kallisto Bustools wrapper (kb) command to create an index
kb kallisto bustools
updated 14 months ago by ★ 7.7k • written 14 months ago by ▴ 110
7
votes
12
replies
2.3k
views
Custom Genome Curation in IGV
IGV
updated 14 months ago by ★ 1.6k • written 14 months ago by ▴ 20
0
votes
4
replies
1.6k
views
Missing Output Exception Error in Snakemake with output directory
Snakemake genome
updated 14 months ago by 45k • written 14 months ago by • 0
2
votes
20
replies
4.0k
views
How to produce a single joint-called VCF file using as input three WGS samples (VCF,CRAM,FASTQ)
VCF WGS
updated 14 months ago by 45k • written 14 months ago by • 0
2
votes
2
replies
989
views
Is the 10X multiome chemistry most similar similar to 10XV1, 10XV2, or 10XV3?
snRNAseq kallisto 10X
14 months ago by biotrekker ▴ 110
1
vote
3
replies
1.2k
views
Estimating per-variant heritability from summary stats
Variants SNP GWAS
updated 14 months ago by 4.8k • written 14 months ago by ▴ 10
2
votes
5
replies
2.7k
views
10X #3' RNA seq - How is strandedness determined?
scRNA-seq
updated 14 months ago by 45k • written 14 months ago by • 0
2
votes
2
replies
2.7k
views
Mugsy alignment of 2 genomes
genome alignment
updated 14 months ago by • 0 • written 8.6 years ago by ▴ 10
0
votes
0
replies
395
views
Mugsy aligner kills alignment with "can't find species error"
aligner mugsy WGA
updated 14 months ago by 45k • written 14 months ago by • 0
7
votes
9
replies
1.9k
views
Gene enrichment tools options
DAVID ShinyGo gene-enrichment
updated 14 months ago by ▴ 470 • written 14 months ago by • 0
121,926 results • Page 89 of 2439
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Comment: cellranger mkref fail/error
gnomAD: query utilitites
Answer: How to overcome OS return value: 4 with SPAdes
Answer: How to overcome OS return value: 4 with SPAdes
Answer: How to overcome OS return value: 4 with SPAdes
Comment: Genome Assembly QC from BAM files
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Great Question to pedro.silvestre • 0
Recent Replies
Answer: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by Vittorio • 0
Joining the convo a bit late, but I found it super useful since I am struggling to analyze MGI data myself. For the library prep used in th…
Comment: How to overcome OS return value: 4 with SPAdes by marongiu.luigi ▴ 760
Yep, that was it. I was using a G:-sync folder... Thank you.
Comment: Help with Model by i.sudbery 22k
There is no way to "code" this directly. Your problem is mathematics, not programming. Standard stochastic models deal with a set of sta…
Answer: How to overcome OS return value: 4 with SPAdes by GenoMax 153k
I am going to hazard a guess that the spaces and email address in file path (you may want to redact your email from post above) is causing …
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 153k
Are you trying to reproduce the assembly result? If not, the complete assembly is already available at NCBI: https://www.ncbi.nlm.nih.gov…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
This may be another example where the assembly you obtained may be better than an existing one .. certainly as far as the accessory chromos…
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
There are some reference assemblies. Some close ones are at chromosome level but exact reference are not chromosome level assemblies. Othe…
Comment: Understanding the relationship between hhr and a3m output of HHblits by Joe 22k
Nice detective work! :)
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
The SRA accession is SRX12366993
Comment: SNP calling with bacterial assembled genome by GenoMax 153k
> After I find some differences between the assembly and the reference, how can I decide confident variants without the depth? Don't think…
Comment: Orthofinder Not Mapping to Any Orthogroups by Philipp Bayer 8.9k
Did you check whether your species' fasta file is named correctly? From memory Orthofinder will pull in files ending in .fa and .fasta in t…
Comment: SNP calling with bacterial assembled genome by yesquokkan • 0
Thank you for your kind answer. May I ask some following questions. However, I only have full access to assembled genomes, and some to ra…
Answer: Understanding the relationship between hhr and a3m output of HHblits by Andrew ▴ 10
Ok after reviewing the HHBlits source code I realize the issue is that the hhr file and the a3m file contain apples and oranges, and it doe…
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I checked the file and it's definitely proteins. I had previously run BUSCO on protein mode on the same file and got >90% completeness. I r…
Comment: Orthofinder Not Mapping to Any Orthogroups by saamhasan55 ▴ 10
I ran BUSCO on the predicted proteome in protein mode and got >91% completeness. I also removed multiple isoforms from the same gene.
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