Example FilesΒΆ
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 regionsOther 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