Generate some random reads for testing.

Using Yeast genes:

ftp://ftp.ensembl.org/pub/release-91/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.I.fa.gz
ftp://ftp.ensembl.org/pub/release-91/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.91.gtf.gz

gzip -d Sac*.gz

Pick only chromosome I genes for this test.

  578  grep "^I	" Saccharomyces_cerevisiae.R64-1-1.91.gtf > chrI.gtf

Pick a subset. Tried random subsets, but it didn't work

  582  gshuf -n 100 chrI.gtf > chrI-100.gtf

Try head instead.

head -n 104 chrI.gtf > chrI-100.gtf

The gtf file has only chromosome number in column 1, the genome
filenames have to match this column.

  584  ln -s Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.I.fa I.fa

Run flux simulator

  585  ~/src/dmel/flux-simulator-1.2/bin/flux-simulator -p small1.par -x -l -s