Open priyanka-surana opened 2 years ago
According to this paper "mappability' = "the fraction of reads derived from a transcript that aligned to the original transcript" so I think this just involves taking the FASTA + GFF and extracting out the transcripts (as FASTA)
Some various tools I found so far:
Could be worth doing some benchmarking to whittle out the 'slow' options? If the tools allows you to supply the transcript boundaries as bed or similar that might be a nice feature rather than extracting the transcriptome beforehand?
Description of feature
This is ideally done with RNA-seq data. It is equal to percentage of reads mapped to the genome. Possible software: WGSIM