Published February 19, 2024 | Version v1
Software documentation Open

ASTA-Seq (Allele-Specific Targeted Amplicon Sequencing)

  • 1. ROR icon Centre for Genomic Regulation

Description

ASTA-Seq (Allele-Specific Targeted Amplicon Sequencing) is an automatical pipeline implemented in two Perl scripts to extract and summarize information from FASTQ reads containing information about the allele-specific (hydroxy)methylation status of regions surrounding several Differentially (hydroxy)Methylated CpGs in X-reactivating gene promoters by DNA methylation arrays. Regions to be analyzed were selected to include species-specific SNPs and at least one D(h)MP while maintaining an amplicon size of 200-500 bp, and escapee gene controls were included as well. Paired oxidative Bisulfite (OxBS) and the mock-oxidation reaction (Bisulfite, BS) treated DNA from day 5 reprogramming samples were used as templates for a two-step PCR amplification protocol before library preparation for high-throughput sequencing.

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Additional details

Software

Repository URL
https://github.com/eblancoga/ASTA-Seq
Programming language
Perl
Development Status
Active