Example Files 
=============

| We have provided the following example files
  `here <https://people.ucsc.edu/~atang14/flair/example_files/>`__:
| - ``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 <http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz>`__
  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 <https://github.com/nanopore-wgs-consortium/NA12878/blob/master/RNA.md>`__
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 <https://github.com/BrooksLabUCSC/labtools/blob/master/NanoSim_Wrapper.py>`__,
a wrapper script written for simulating nanopore transcriptome data
using `Nanosim <https://github.com/bcgsc/NanoSim>`__