Question: NGS Pathway analysis for Trio
0
gravatar for nayshool
3.8 years ago by
nayshool20
Israel
nayshool20 wrote:

Hi everyone!

 

I am looking for a tool for pathway analysis of next generation sequencing data of a trio (the child is sick with some neurological disease). Does anyone have recommended tool or tools for such a task?

 

Thank you

 

Omri

snp tool next-gen • 1.2k views
ADD COMMENTlink modified 3.8 years ago by RamRS24k • written 3.8 years ago by nayshool20
1
gravatar for RamRS
3.8 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

You're looking for a pipeline, not a tool. You will have to go through the routine of QC, alignment and variant calling and then use a pedigree to phase the variants, then annotate using KEGG/GO databases before moving on to pathway enrichment analyses. 

ADD COMMENTlink written 3.8 years ago by RamRS24k

regarding the last step u mentioned, after phasing the mutations, is there a pathway analysis tool that takes into consideration if the mutations are from a paternal or a maternal origin ?

ADD REPLYlink written 23 months ago by lait140

You might want to check out PLINK/SEQ's denovo and cnv-denovo utilities

ADD REPLYlink written 23 months ago by RamRS24k
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