Question: ides capp-seq bioinformatics pipeline
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I am new in bioinformatics. we would like to apply the iDES-enhanced CAPP-Seq (CAncer Personalized Profiling by deep Sequencing), however, I have few questions about the procedures after read those papers. I sincerely wish someone can help me for this.

capp-seq paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016134/

ides capp-seq paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907374/

For capp-seq, the bioinformatics pipeline is from BWA (alignment) -> SAMtools (sort and index) -> custom Perl script for QC (statistics, mapping charactersics, read quality including SAMtools flagstat, FASTQC, BEDtools coverageBED) -> Varscan2 (SNVs/Indels) AND FACTERA (fusions) -> compare allele frequency with paired samples ? (fisher test) -> Seattle (annotation) -> compare ctDNA variants to other ctDNA in the same position ? (fisher test)

I am not sure is it correct, please feel free to comment.

However, for ides capp-seq, I dont know how to implement the duplex barcode and background polishing packages for the above procedure.

iDES (Integrated Digital Error Suppression):

https://cappseq.stanford.edu/ides/download.php#overview

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