Demultiplexing 2015 Data

In [1]:

CUROUT=$HOME/work/scratch/2015_output_all_data
DEMUX=$CUROUT/demux_fastqs
CURDATA=/data/HTS_2015_data/runs_combined
INFO=$CURDATA

mkdir -p $DEMUX

In [2]:

ls $INFO

ls: /data/HTS_2015_data/runs_combined: No such file or directory







In [3]:





GROUP=dryrun
fastq-multx -m1 -d1 -x -B ${INFO}/dryrun_barcodes.tab \
    ${CURDATA}/${GROUP}_combined_I1.fastq.gz \
    ${CURDATA}/${GROUP}_combined_R1.fastq.gz \
    ${CURDATA}/${GROUP}_combined_R2.fastq.gz \
    -o ${DEMUX}/i1.%.fq.gz ${DEMUX}/r1.%.fq.gz ${DEMUX}/r2.%.fq.gz \
    > ${DEMUX}/${GROUP}_demux_summary.txt















Error opening file '/data/HTS_2015_data/runs_combined/dryrun_barcodes.tab': No such file or directory



















In [4]:





GROUP=KNP
fastq-multx -m1 -d1 -x -B ${INFO}/groups_KNP_barcodes.tab \
    ${CURDATA}/groups_${GROUP}_combined_I1.fastq.gz \
    ${CURDATA}/groups_${GROUP}_combined_R1.fastq.gz \
    ${CURDATA}/groups_${GROUP}_combined_R2.fastq.gz \
    -o ${DEMUX}/i1.%.fq.gz ${DEMUX}/r1.%.fq.gz ${DEMUX}/r2.%.fq.gz \
    > ${DEMUX}/${GROUP}_demux_summary.txt















Error opening file '/data/HTS_2015_data/runs_combined/groups_KNP_barcodes.tab': No such file or directory

















Now we can run pool2 - remember to use groups_EG_barcodes.tab
instead of groups_KNP_barcodes.tab




In [5]:





GROUP=EG
fastq-multx -m1 -d1 -x -B ${INFO}/groups_EG_barcodes.tab \
    ${CURDATA}/groups_${GROUP}_combined_I1.fastq.gz \
    ${CURDATA}/groups_${GROUP}_combined_R1.fastq.gz \
    ${CURDATA}/groups_${GROUP}_combined_R2.fastq.gz \
    -o ${DEMUX}/i1.%.fq.gz ${DEMUX}/r1.%.fq.gz ${DEMUX}/r2.%.fq.gz \
    > ${DEMUX}/${GROUP}_demux_summary.txt















Error opening file '/data/HTS_2015_data/runs_combined/groups_EG_barcodes.tab': No such file or directory



















In [6]:





ls ${DEMUX}















EG_demux_summary.txt            dryrun_demux_summary.txt
KNP_demux_summary.txt