DNASeq pipeline analysis

Hello All,

Can anyone please refer me to a DNAseq pipeline? I need to develop the pipeline from scratch. I have done SNP/indel calling, though have not worked with a DNAseq data before.

Appreciate it,

rna dneseq

• 143 views • link

updated 3 months ago by ATpoint

• written 3 months ago by SHN •

1 answer

nf-core sarek in terms of things you could possible include. Get good AI help, it is really good at these sorts of things and can accelerate progress a lot.

• 0 views • link

written 3 months ago by ATpoint

More posts like this

eQTL analysis -- SNP associations at different chromosomes
written 4.4 years ago by SHN •

Hi All, I have a quick question regarding the eQTL analysis. I am mainly looking for cis-eqtls. So I extracted all the SNPs at 500 …
SNP filtering
written 5.0 years ago by rheab1230 •

Hello everyone, I am trying to filter .vcf files to contain only single point SNP and remove indel. I have remove indel from the .vcf …
Tools for SNPs and Indels (RNA seq. Nanopore)
written 5.2 years ago by mailard •

Hello! Can you commend me for tools that calling SNP and Indel for nanopore data? I know about madaka and isONclust2, but I cannot understand …
SNP calling and SNP discovery
written 6.8 years ago by a.hasankhani74 •

Hi please give me a pipeline for SNP calling and SNP discovery using RNAseq data
priors for calculting genotype likelihood using RNAseq data
written 9.2 years ago by prasundutta87

Can anyone point me to a literature or explain the need of population priors during genotype likelihood estimation using RNAseq data? I did get results …
Multiple RNAseq Library to SNP Call using GATK
written 9.3 years ago by Bioinfonext

1) I want to run star 2 pass pipeline: After running 1-star mapping, I got SJ.OUT.TAB for each library , now please suggest after concatenate …
multi vcf population genomics analysis
written 9.5 years ago by guillaume.rbt

Hi all, I have done an indel and SNPs calling on multiple strains of a fungus, with WGS data. I have now a multi vcf …
Job: [Moderators] SNP website Development Site
written 9.6 years ago by rapidracing911 •

Hello, I'm looking to see if their is anyone who may develop SNP site which data will be uploaded to it and from their determine …
SAMtools mpileup and bcftools doesn't call InDels...
written 11.1 years ago by Kirill Tsyganov

Hi Guys, I have been researching fair bit over the last few days about SNPs/InDels calling, My project pretty much exactly summarised [here][1]. My NGS …
Illumina Ngs Test Data For Snp/Indel Calling And Association Study
written 15.2 years ago by Travis

Hi all, I am currently attempting to create a pipeline for Illumina NGS sequence alignment, SNP/Indel-calling and association testing upon multiple samples. Can anyone …