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121,924 results • Page 79 of 2439
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Differential expression Analysis of PacBio Isoseq data
Differential-Expression-Analysis ISOseq
13 months ago by tvibhaps ▴ 10
0
votes
1
reply
702
views
Book about RNA structure
RNA
updated 13 months ago by ★ 30k • written 13 months ago by • 0
0
votes
2
replies
792
views
eagle: error: argument command: invalid choice: 'DATASET_chr_for_phasing.vcf.gz' (choose from 'interface', 'convert')
GWAS-Imputation
13 months ago by nareshmvr ▴ 10
0
votes
0
replies
556
views
whatshap ploidy error on female sample
ONT ploidy phasing nanopore
updated 13 months ago by 45k • written 13 months ago by ▴ 110
0
votes
0
replies
419
views
ROSE analysis is empty
ChIP-seq H3K27ac ROSE
13 months ago by pb11 ▴ 30
1
vote
0
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424
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Seeking Advice on Protein Evidence for GALBA Annotation of Non-Model Rodent Genome
Annotation GALBA MAKER Genome BREAKER
13 months ago by aleponce • 0
5
votes
4
replies
2.2k
views
difference between macs2 callpeak using bam and bed file
macs2 atac-seq
13 months ago by QX ▴ 80
2
votes
1
reply
564
views
Reference source that provides IRIs for Ensembl gene IDs?
Ensembl IRI
updated 13 months ago by 153k • written 13 months ago by ▴ 80
1
vote
1
reply
756
views
Can i use population as a trait to perform GWAS?
Hapmap PLINK GWAS QC
updated 13 months ago by ★ 3.1k • written 13 months ago by ▴ 10
14
votes
15
replies
3.7k
views
How to give 2 input files (one from the process before and one from 3 processes before) in nextflow pipeline?
nextflow nf-core processes channels
updated 13 months ago by 7.9k • written 13 months ago by ▴ 30
0
votes
0
replies
416
views
Should I plot with methylDiff or methylBase object?
MethylKit
13 months ago by CTLong ▴ 140
0
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5
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1.7k
views
Differential gene expression (aiming to create heatmap) for raw RNAseq count data from different publications - how to?
R DESeq2 Differential-expression
updated 13 months ago by ★ 2.1k • written 13 months ago by • 0
5
votes
18
replies
4.3k
views
Forum: Is "training", fine tuning, or overfitting on "external independent validation datasets" considered cheating or scientific misconduct?
tools scientific misconduct overfitting
13 months ago by ivicts ▴ 10
2
votes
5
replies
1.3k
views
call peak for all replicates in all conditions using macs2
macs2 ATACseq
updated 13 months ago by ▴ 150 • written 13 months ago by ▴ 80
0
votes
0
replies
531
views
Are equal whisker lengths important in an RLE plot?
EDA plot RNAseq EDAseq RLE
13 months ago by BioinfGuru ★ 2.1k
1
vote
4
replies
989
views
trimming 151bp to shorter k-mer in ATAC-seq analysis
ATAC-seq
13 months ago by QX ▴ 80
67
votes
15
replies
52k
views
13 follow
Get chromosome sizes from fasta file
genome ucsc
updated 13 months ago by ★ 2.2k • written 9.7 years ago by ▴ 750
101
votes
20
replies
84k
views
14 follow
Sequence length from Fasta
fasta
updated 4 months ago by • 0 • written 10.9 years ago by ▴ 90
1
vote
3
replies
1.8k
views
Merged Reference Panel using WES data
sequencing imputation reference
updated 13 months ago by 153k • written 5.9 years ago by • 0
8
votes
4
replies
5.1k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 13 months ago by • 0 • written 3.1 years ago by 89k
0
votes
0
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414
views
How can I visualise the gene order for fungal mitogenomes?
mitogenome fungal genomics
13 months ago by madders73 ▴ 10
0
votes
3
replies
982
views
flipped BAM files in IGV after STAR aligner
IGV aligner STAR BAM RNA-seq
updated 13 months ago by ★ 1.6k • written 13 months ago by • 0
4
votes
2
replies
1.1k
views
Integration of scRNA-seq datasets from different tissues
scRNA-seq
updated 13 months ago by ▴ 100 • written 14 months ago by ▴ 10
1
vote
3
replies
1.1k
views
Canu Nanopore Genome assembly optimization
slurm assembly genome canu nanopore
updated 13 months ago by ★ 2.2k • written 13 months ago by ▴ 240
0
votes
3
replies
1.1k
views
Relative abundance of plasmid DNA content in each sample
Illumina E.coli WGS
13 months ago by adarsh ▴ 60
0
votes
0
replies
396
views
Tool: TCGA-DDR: A tool for Survival and Genomic feature analysis
damage DDR TCGA DNA survival
13 months ago by camelia.mocanu • 0
1
vote
2
replies
1.1k
views
How to fix this error while performing QC in PLINK "Warning: 228 het. haploid genotypes present"
Hapmap PLINK GWAS QC
13 months ago by Yugan Gogul Muthukumar ▴ 10
1
vote
2
replies
699
views
Remove specific reads from a metagenomic sequencing run
metagenomics
updated 13 months ago by 7.9k • written 13 months ago by ▴ 140
0
votes
1
reply
504
views
How can you separate and ignore the expression changes caused by single cell isolation from the single cell transcriptome ?
cell single trancriptome
updated 13 months ago by ★ 7.7k • written 13 months ago by • 0
1
vote
4
replies
1.2k
views
EdgeR gmlQLF with low number of genes
edgeR DGE Pseudobulking
updated 13 months ago by ★ 8.3k • written 13 months ago by • 0
0
votes
0
replies
704
views
Job: Senior Scientist position (m/f/d) computational biology/bioinformatics at UKSH Prof. Martin Kircher
Bioinformatics genomics
13 months ago by alwayshope ▴ 40
2
votes
3
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1.0k
views
How to generate GFF3 or GTF files for a custom reference.
GFF3 GTF
updated 13 months ago by 45k • written 13 months ago by • 0
0
votes
6
replies
1.5k
views
Batch correction for RNA-seq using ComBat-seq for same group and batch
SVA ComBat_seq ComBat DESeq2 RNA-seq
13 months ago by botloggy ▴ 10
3
votes
5
replies
1.1k
views
Any recommended way to share ChIP track to collaborator through UCSC browser without using local FTP?
ChIP-Seq UCSC-genome-browser
13 months ago by Pei ▴ 240
1
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2
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1.2k
views
topGO R package - how to account for fold expression and p value
R proteomics topGO enrichment
13 months ago by Sven • 0
12
votes
5
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2.1k
views
Forum: Books and Blogs guiding the programming practice in bioinformatic research?
R Python Programming
13 months ago by JustinZhang ▴ 140
2
votes
1
reply
543
views
Assembly of chloroplast genome from plant WGS
Plant assembly chloroplast Illumina WGS
updated 13 months ago by 153k • written 13 months ago by ▴ 60
2
votes
5
replies
1.1k
views
Combining Overlapping ATC Code Usage in R
R pharmacogenetics
13 months ago by d.s.zimmerman • 0
0
votes
0
replies
622
views
News: Intro to Linux for Genomics Online Course
linux workshop genomics
updated 13 months ago by 45k • written 13 months ago by ▴ 10
2
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7
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1.8k
views
BUSCO v3 eukaryotic database
genome assembly BUSCO
updated 13 months ago by 153k • written 20 months ago by • 0
0
votes
0
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731
views
Somatic variant filtering necessary files
GetPileupSummaries
13 months ago by Anitha ▴ 10
0
votes
0
replies
316
views
Blog: Posey Lab: Beyond Replication with scRNA-seq Analysis in g.nome®
software platform
updated 13 months ago by 45k • written 13 months ago by • 0
1
vote
1
reply
628
views
Testing for specific genes of whole RNA Sequencing
R DESeq2 Sequencing RNA
updated 13 months ago by 89k • written 13 months ago by ▴ 20
1
vote
3
replies
816
views
RNA seq data analysis
RNA-seq
updated 13 months ago by 45k • written 13 months ago by • 0
1
vote
11
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1.5k
views
Use R to Produce CpG Information
R CpG
13 months ago by Dana • 0
0
votes
0
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617
views
Job: Researcher (m/w/d) in Data Management and Bioinformatics - LIED AG Prof. Busch
Data management Researcher
13 months ago by alwayshope ▴ 40
3
votes
4
replies
1.2k
views
Need help with design/workflow please?
deseq2 batch workflow
13 months ago by BioinfGuru ★ 2.1k
0
votes
0
replies
439
views
News: Course: Structural Variant Detection and Comparison
Structural-Variants SVs Nanopore
13 months ago by Physalia-courses ★ 2.6k
0
votes
0
replies
458
views
News: Course: Transform your data into an interactive web app with R Shiny
Rshiny Dataviz Course
13 months ago by Transmitting Science communication ▴ 70
0
votes
1
reply
463
views
What may cause my z-score-FDR distribution
FDR Z-score CRISPR_screen
updated 13 months ago by 89k • written 13 months ago by • 0
121,924 results • Page 79 of 2439
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Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
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Recent Replies
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.
Comment: Help with Model by Stele • 0
Hey, thanks for the reply! I think I didn't make the question very understandable. I do know how to code for this, the wall I have hit is *…
Comment: Orthofinder Not Mapping to Any Orthogroups by Mensur Dlakic ★ 30k
Not enough detail to make a definitive recommendation. Since this should not happen, an educated guess is that you are doing something wron…
Comment: Orthofinder Not Mapping to Any Orthogroups by Michael 56k
A reason may be that your gene prediction is off. Did you run BUSCO on your predicted proteome? If the gene prediction is ok, then you shou…
Comment: Genome Assembly QC from BAM files by GenoMax 153k
> Can you comment on these, If they look good ? More importantly how do these assemblies compare (contiguous/number of chromosomes/size) t…
Comment: TOPMed Imputation - More than 10000 allele switches by Qianshu • 0
Hi, I have the same error with you, have you sorted it out yet? If you have, could you please share some? Thank you!
Comment: Genome Assembly QC from BAM files by colindaven 7.9k
yes they look excellent
Comment: Genome Assembly QC from BAM files by SomeOne ▴ 240
hello @colindaven I ran the INSPECTOR tool you mentioned on the genome assemblies. Below are stats for one of my sample (othere were simi…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by Christopher ▴ 10
You are right. I initially decided to keep Cutadapt because I feel more confident using it for primer removal, and it is the tool most comm…
Answer: Help with Model by i.sudbery 22k
I'm not quite sure what you are asking. Stochastic reaction networks like this can be coded using the Gillespie algorithm. Genes being …
Comment: miRNA low mapping ratings by Ant ▴ 50
No, these are from the total reads, but when considering only the reads with adapter, I checked MultiQC again and it’s around 10–20% when a…
Comment: miRNA low mapping ratings by GenoMax 153k
> the total number of reads is very low (around 1–10% of the total reads) Are these the reads that actually have the QIAseq 3'-miRNA adapt…
Comment: Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken? by GenoMax 153k
> cutadapt > bbduk > bowtie2 > qiime2 > dada2 > kraken2 > krona Curious as to why you have `cutadapt` and `bbduk`. `bbduk` should be able…
Comment: miRNA low mapping ratings by i.sudbery 22k
As GenoMax said, the most likely thing to me here is that there is nothing cloned into the library. I can't think of any bioinformatic reas…
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