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