Has anyone got sample R workflow to analyze paired end illumina DNA seq data to find variations and SNPs?

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Shaojun Xie

I didn't use R workflow to do variation calling. But I came across Bioconductor workflow. Hope it can help you.

https://www.bioconductor.org/help/workflows/

https://www.bioconductor.org/help/course-materials/2014/BioC2014/Lawrence_Tutorial.pdf

Romit Seth

Hello Sanjay,

You can use kissplice2reftranscriptome or kissplice2refgenome tool to ascertain SNPs using denovo assembly or reference based assembly respectively. The output would provide you single SNP, Multiple SNPs, INDELs and alternative splice sites. Further you can also predict that whether your SNP is condition specific by using kissDE which is a R based script. Hope this would help you and makes your analysis easier.

Kindly follow the link below

http://kissplice.prabi.fr/tools/kiss2rt/

Mendem suresh kumar

www.patricbio.org.----free online server.

you can do basic genomic works And variant analysis.

Laith Al-Ani

Hi Sanjay

Several helpful references on attachment 1

https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2013/131021_HTS/genesandgenomes.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490498/

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

https://www.illumina.com/documents/products/datasheets/datasheet_genomic_sequence.pdf

https://onlinelibrary.wiley.com/doi/10.1111/eva.12178/full

https://chagall.med.cornell.edu/galaxy/GalaxyWorkshopNotes.pdf

https://academic.oup.com/bib/article/15/2/256/210976/A-survey-of-tools-for-variant-analysis-of-next

https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools

https://www.sanger.ac.uk/generic-detail/esgi-high-throughput-sequencing-analysis-tools

https://github.com/NCBI-Hackathons/Community_Software_Tools_for_NGS/blob/master/NGS_Tools_List.md

https://www.sciencedirect.com/science/article/pii/S1874778716300368

https://www.mi.fu-berlin.de/en/inf/groups/abi/theses/master_dipl/krakau/msc_thesis_krakau.pdf

https://f1000research.com/articles/5-1542/v2

https://www.epigenesys.eu/images/stories/protocols/pdf/20150303161357_p67.pdf

https://www.hindawi.com/journals/ijpg/2012/831460/

https://www.bioconductor.org/help/workflows/methylationArrayAnalysis/

https://www.personal.psu.edu/iua1/courses/2013-BMMB-597D.html

https://web.stanford.edu/group/wonglab/doc/RNA-seq-talk-JSM2010.pdf

https://bfg.oxfordjournals.org/content/9/5-6/416.full

https://www.sevenbridges.com/wp-content/uploads/2016/11/WP_Scalable_Web.pdf