==== description ====
The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. Software page : [[https://github.com/smithlabcode/preseq]].

==== software version ====
Bellow description covers preseq version 2.3.1 .

==== prepare software ====
Login to anthill23, start interactive session in which download and compile preseq ((this will take 3 minutes)):

  @anthill23:~$ srun -n 2 --mem=4G --pty bash -l
  
  mkdir ~/anthill23_soft/
  cd ~/anthill23_soft/
  wget -O preseq-3.1.2.tar.gz https://github.com/smithlabcode/preseq/releases/download/v3.1.2/preseq-3.1.2.tar.gz
  tar xvzf preseq-3.1.2.tar.gz
  cd preseq-3.1.2
  
  mkdir build
  cd build
  
  mkdir -p /home/users/${USER}/anthill23_preseq/preseq-3.1.2
  ../configure --prefix="/home/users/${USER}/anthill23_preseq/preseq-3.1.2" --enable-hts
  
  make -j${SLURM_NPROCS} && make install 
  
  #read output
  
  #exit interactive mode when finished with exit command
  exit


==== sbatch example ====
This description assumes that above step ( prepare software ) were done beforehand. \\
Bellow slurm job creates temporary folder in your home folder (like ''tmp.AtrQrrJi3W''), then downloads file ''wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam'' and run preseq on it ((this will take 2 minutes)). \\
Inspect job output ex.: ''slurm-1949.out'' and ''yield_estimates.txt'' file for preseq output messages and output.

File ''preseq_test.sbatch'' :

<code>
#!/bin/bash -l
#SBATCH --partition=test
#SBATCH --ntasks=2
#SBATCH --mem 4G
#SBATCH --job-name preseq_test

#prepare temporary folder
cd `mktemp -d -p ~/`

#download bam filefq file
wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam

#export path to preseq-3.1.2 binary
export PATH=$PATH:/home/users/${USER}/anthill23_preseq/preseq-3.1.2/bin

#predict the yield of a future experiment if the input file is in .bam format
preseq lc_extrap -B -o yield_estimates.txt wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam

</code>

==== performance tests ====
None. At this time.