AmpliconSeqQualityFilter

Last login: Fri Feb 28 08:44:34 on ttys002
abt6-derek-mba:~ dlundberg$ combined_fasta_name="HiSeq0168_all_trimmed.fasta"
abt6-derek-mba:~ dlundberg$ $combined_fasta_name
-bash: HiSeq0168_all_trimmed.fasta: command not found
abt6-derek-mba:~ dlundberg$ 
abt6-derek-mba:~ dlundberg$ burrit
dlundberg@burrito.eb.local's password: 
Last login: Thu Feb 27 20:24:42 2020 from 10.1.5.120
dlundberg@burrito:~$ proj7
dlundberg@burrito:/ebio/abt6_projects7/bacterial_strain_analysis$ cd /ebio/abt6_projects7/bacterial_strain_analysis/code/HiSeqTrim_LOAD.sh
-bash: cd: /ebio/abt6_projects7/bacterial_strain_analysis/code/HiSeqTrim_LOAD.sh: Not a directory
dlundberg@burrito:/ebio/abt6_projects7/bacterial_strain_analysis$ vi /ebio/abt6_projects7/bacterial_strain_analysis/code/HiSeqTrim_LOAD.sh
















dlundberg@burrito:/ebio/abt6_projects7/bacterial_strain_analysis$ 
dlundberg@burrito:/ebio/abt6_projects7/bacterial_strain_analysis$ vi /ebio/abt6_projects7/bacterial_strain_analysis/code/MiSeqQualityFilter.sh 







#!/bin/sh
#
#  Reserve 1 CPUs for this job
#$ -pe parallel 1
#  Request 10G of RAM
#$ -l h_vmem=10G
#
#  The name shown in the qstat output and in the output file(s). The
#  default is to use the script name.
# -N $name
#
#  The path used for the standard output stream of the job
# -o /ebio/abt6_projects7/bacterial_strain_analysis/data/processed_DATA
#
# Merge stdout and stderr. The job will create only one output file which
# contains both the real output and the error messages.
# -j y
#
#  Use /bin/bash to execute this script
#$ -S /bin/bash
#
#  Run job from current working directory
#$ -cwd
#
#  Send email when the job begins, ends, aborts, or is suspended
##$ -m beas

fq=$1
usearch=/ebio/abt6_projects7/bacterial_strain_analysis/code/usearch10

echo $fq
$usearch -fastq_filter "$fq" -fastq_maxee 1.0 -relabel @ -fastaout "$fq"_filtered.fa -fastqout_discarded "$fq"_trash