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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Discordant alignments and -y option in PE ATAC-Seq experiment #77

Closed uli-arb closed 2 years ago

uli-arb commented 2 years ago

Hello,

I'm not sure if this is the best place to ask this, but I'm not sure about when to include discordant or half-alignments during peak calling. Is the -y option intended for mainly single-end processing? In what kind of situations would only one of the PE reads be aligning to the genome? Thank you for your help and developing Genrich!

jsh58 commented 2 years ago

Thanks for the question. The -y (or -w <int>) option is required to analyze single-end reads, but certainly can be used with paired-end reads as well. Paired-end reads may have excessive unpaired alignments under a variety of circumstances, such as low-quality reads (often R2), or an incomplete reference genome.