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.
Bellow description covers preseq version 2.3.1 .
Login to anthill23, start interactive session in which download and compile preseq 1):
@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${SLURM_NPROCS} && make install #read output #exit interactive mode when finished with exit command exit
This description assumes that above step ( prepare software ) were done beforehand.
Bellow slurm job creates temporary folder in your home folder (like tmp.AtrQrrJi3W
), then downloads file wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam
and run preseq on it 2).
Inspect job output ex.: slurm-1949.out
and yield_estimates.txt
file for preseq output messages and output.
File preseq_test.sbatch
:
#!/bin/bash -l #SBATCH --partition=test #SBATCH --ntasks=2 #SBATCH --mem 4G #SBATCH --job-name preseq_test #prepare temporary folder cd `mktemp -d -p ~/` #download bam filefq file wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam #export path to preseq-3.1.2 binary export PATH=$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
None. At this time.