This is an old revision of the document!
description
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. Software page : https://github.com/MikkelSchubert/adapterremoval, software usage examples https://adapterremoval.readthedocs.io/en/latest/examples.html .
software version
Bellow description covers AdapterRemoval version 2.3.1 .
prepare software
Login to anthill23, start interactive session in which download and compile AdapterRemoval 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${SLURM_NPROCS} && make install
#read output
#exit interactive mode when finished with exit command
exit
sbatch example
This description assumes that above step ( prepare software ) were done beforehand.
Bellow slurm job creates temporary folder in your home folder (like tmp.AtrQrrJi3W), then downloads file wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam and run preseq on it. This job will take about 10 minutes, inspect job output ex.: slurm-1949.out for preseq output messages.
File preseq_test.sbatch :
#!/bin/bash -l
#SBATCH --partition=test
#SBATCH --ntasks=2
#SBATCH --mem 4G
#SBATCH --job-name preseq_test
#prepare temporary folder
cd `mktemp -d -p ~/`
#download bam filefq file
wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrRnaSeq/wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1.bam
#export path to preseq-3.1.2 binary
export PATH=$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
performance tests
None. At this time.