Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency
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@PanosProv is already working on this.
Since Nov 11, 2024.
enhancement
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Description
Description of feature
Library preparation kits come with unmethylated and methylated DNA controls that are added to samples (e.g. NEBNext EM-seq). It would be useful to supply methylseq with the fasta sequences of the controls and have it perform additional alignment, deduplication, and extraction using those references. This would help enable calculation of bisulfite/enzymatic conversion efficiency.
Thank you for providing this excellent pipeline!
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