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121,934 results • Page 115 of 2439
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0
votes
1
reply
693
views
filtering before dada2
bbduk qiime2 dada2 metagenomic
updated 17 months ago by 45k • written 17 months ago by • 0
0
votes
6
replies
1.5k
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 17 months ago by 15k • written 17 months ago by • 0
1
vote
4
replies
1.3k
views
TaxID mapping file
annotation blobtools RNAseq decontamination transcriptomes
updated 5 months ago by • 0 • written 17 months ago by ▴ 40
1
vote
0
replies
476
views
.lgen file has 3+ different alleles
PLINK lgen ped
updated 16 months ago by 12k • written 17 months ago by ▴ 10
0
votes
0
replies
419
views
vcf procesing for ML antigen prediction
formats vcf fastaq HLA_imputation HLA_typing
17 months ago by Javier • 0
0
votes
2
replies
935
views
Extracting mutation status from MAF files - TCGA
TCGA maf mutation
updated 16 months ago by ★ 1.3k • written 17 months ago by ▴ 10
0
votes
0
replies
397
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic Variant predisposition
17 months ago by mikemakaveli1 • 0
2
votes
2
replies
818
views
Raw counts using stringtie
stringtie RNA-seq
updated 17 months ago by 154k • written 17 months ago by • 0
0
votes
0
replies
440
views
Modify plot R mtDNA indel
plot mtDNA R
17 months ago by marco.barr ▴ 180
0
votes
0
replies
712
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot graphical_output GSEA clusterProfiler
17 months ago by NorbertK ▴ 10
4
votes
2
replies
1.1k
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 17 months ago by 45k • written 17 months ago by ▴ 50
13
votes
14
replies
3.9k
views
High Malat-1 expression in single cell data
single-cell
updated 16 months ago by ▴ 40 • written 17 months ago by ▴ 50
0
votes
2
replies
690
views
Downloading older version of a tool
Alignment tools
17 months ago by RT • 0
0
votes
0
replies
538
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization illumina ngs sequencing
17 months ago by rustykb ▴ 20
1
vote
1
reply
506
views
DSEQ2 analysis
DESEQ2 logfoldchange
updated 17 months ago by 45k • written 17 months ago by ▴ 10
4
votes
5
replies
2.7k
views
Generating mpileup file using samtools
mpileup samtools
updated 17 months ago by 22k • written 17 months ago by • 0
3
votes
5
replies
5.3k
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 17 months ago by ▴ 490 • written 17 months ago by ▴ 10
1
vote
3
replies
926
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ RNAseq
updated 17 months ago by 89k • written 17 months ago by • 0
0
votes
0
replies
581
views
News: Cellosaurus release 49 is available
cell biocuration line database news knowledgebase
17 months ago by Amos Bairoch ▴ 140
2
votes
3
replies
1.2k
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 17 months ago by ★ 3.1k • written 17 months ago by ▴ 100
0
votes
0
replies
442
views
SIngle cell analysis
Seurat scRNA-seq Harmony DoubletFinder Merge
17 months ago by JY • 0
1
vote
2
replies
1.4k
views
homer not configured properly
Homer makeTagDirectory
updated 17 months ago by ▴ 10 • written 3.4 years ago by • 0
1
vote
3
replies
1.5k
views
Bedtools merge minimum overlap?
bedtools genomics
updated 17 months ago by 36k • written 17 months ago by • 0
0
votes
0
replies
502
views
Empty table plot using plotGseaTable()
FGSEA
17 months ago by Chris ▴ 360
2
votes
1
reply
1.4k
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 17 months ago by ▴ 160 • written 17 months ago by ▴ 10
1
vote
3
replies
1.2k
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 17 months ago by ★ 19k • written 17 months ago by ▴ 10
3
votes
5
replies
1.8k
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
17 months ago by Maverick ▴ 10
3
votes
8
replies
8.3k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 17 months ago by • 0 • written 6.5 years ago by 11k
0
votes
2
replies
717
views
Base Quality Score Recalibration with different reference genome
SNPs GATK BQSR RNA-seq
17 months ago by dtnondorf • 0
3
votes
8
replies
1.7k
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 16 months ago by ▴ 420 • written 17 months ago by ▴ 100
1
vote
2
replies
929
views
RNA-seq data for deep learning classification
rna-seq
17 months ago by yahn ▴ 10
3
votes
8
replies
1.8k
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
16 months ago by Qroid ▴ 40
0
votes
1
reply
1.6k
views
Loss of 'var' using concatenation of AnnData objects
Scanpy AnnData
updated 17 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
522
views
Provean help
variant Provean
updated 17 months ago by ★ 30k • written 17 months ago by • 0
1
vote
1
reply
979
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL GTEx
updated 17 months ago by ★ 3.1k • written 17 months ago by ▴ 20
4
votes
7
replies
1.5k
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
16 months ago by Chen • 0
5
votes
5
replies
1.1k
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 17 months ago by ▴ 40 • written 17 months ago by ▴ 210
1
vote
7
replies
2.1k
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
17 months ago by eebloom ▴ 110
3
votes
3
replies
885
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 17 months ago by 89k • written 17 months ago by • 0
0
votes
0
replies
323
views
Use of annotation of integrated Seurat object in single sample
Seurat
17 months ago by Nona ▴ 90
0
votes
0
replies
405
views
News: Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding Programming R
updated 17 months ago by 45k • written 17 months ago by ★ 2.6k
0
votes
1
reply
739
views
Subsetting and merging back Seurat Object brings different results
Seurat
17 months ago by Nona ▴ 90
0
votes
0
replies
742
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS Genomics Post-doc R-loops
updated 17 months ago by 45k • written 17 months ago by • 0
1
vote
1
reply
573
views
Discrepancy in read counts from fastq
downsampling fastq
updated 17 months ago by 45k • written 17 months ago by ▴ 180
0
votes
0
replies
497
views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
17 months ago by Vijith ▴ 100
10
votes
14
replies
3.2k
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 16 months ago by 154k • written 17 months ago by • 0
0
votes
1
reply
924
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 17 months ago by ▴ 310 • written 17 months ago by • 0
0
votes
0
replies
532
views
Combining Methylation Microarray data from different platforms
Microarray DNA EPIC 450K Methylation
17 months ago by James ▴ 30
0
votes
1
reply
1.1k
views
Basic stats in hierfstat
Fst stats hierfstat
updated 17 months ago by • 0 • written 2.9 years ago by • 0
1
vote
3
replies
906
views
Odd alignment question/finding
Alignment
updated 17 months ago by ★ 2.4k • written 17 months ago by • 0
121,934 results • Page 115 of 2439
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What happened to biomart.org
Answer: allele frequency in VCF
Understanding terms, specifically relating to GT:PL in a VCF file
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Answer: WGCNA package in R: dendogram plot error
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
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Recent Replies
Answer: Linear regression vs DESeq2 models for DEG analysis by swbarnes2 15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
Comment: What happened to biomart.org by Jeremy Leipzig 23k
same with geuvadis.org
Comment: real time PCR data analysis by Gordon Smyth ★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction by Fatemeh ▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis by Fatemeh ▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org by GenoMax 154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis by ATpoint 89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org by ATpoint 89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction by Fatemeh ▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
ATpoint, you are absolutely bang on. In fact, my intention is not to switch careers but to connect with this field and build tools/systems …
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I am trying to reproduce the assembly from the raw pacbio reads. I want to reconstruct the assembly using the pacbio reads only.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by ATpoint 89k
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theore…
Comment: Looking to learn practical bioinformatics by ATpoint 89k
> How do I connect the dots to a grand vision of drug discovery, DNA analysis, disease etc. Despite that computational-driven data analys…
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
Thank you, genomax, for the recommendations! Very helpful!
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