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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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minimap2 step: input and reference files #11

Closed sdwien closed 5 years ago

sdwien commented 5 years ago

In the example command for minimap2, you use the output of NanoFilt instead of the U>T converted fastq, is that correct? Also, I assume you use a transcriptome fasta as input for minimap2, right? Thank you, best, Sophia

Huanle commented 5 years ago

@sdwien In the example, U>T conversiont was carried out before nanofilt, so converted fastqs were mapped with minimap2. And yes, a reference transcriptome should be used. Otherwise, a reference genome will also wokr if alternative splicing is 'very' rare.