Example Files

We have provided the following example files here:

• star.firstpass.gm12878.junctions.3.tab, a file of splice junctions observed from short read sequencing of GM18278 that can be used in the correction step with -j. Junctions with fewer than 3 uniquely mapping reads have been filtered out.

• promoter.gencode.v27.20.bed, promoter regions determined from ENCODE promoter chromatin states for GM12878 and 20 bp around annotated TSS in GENCODE v27. Can be supplied to flair-collapse with -p to build the initial firstpass set with only reads with start positions falling within these regions

Other downloads:

• Native RNA Pass reads Running these 10 million nanopore reads from fastq through flair align, correct, and collapse modules to assembled isoforms with 8 threads requires ~3.5 hours (includes ~2.5 hours of minimap2 alignment)

• NanoSim_Wrapper.py, a wrapper script written for simulating nanopore transcriptome data using Nanosim