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eolesin edited this page Jan 11, 2021 · 13 revisions

Examining diversity of rRNA genes within the quality filtered reads.

# Define path to reads
PATH_READS2="01_QC"

# Define path to the database
PATH_DB="/export/dahlefs/work/Databases/Phyloflash_db/138/"

# Run phyloseq on the reads
# I wanted to simultaneously change the names of the files from here too... 
for file in ${PATH_READS2}/*R1.fastq;
    do   
    nam=$(basename ${file} | rev | cut -f2- -d"-" | rev | cut -f2- -d"-"); \
    firstbit=$(basename ${file} | cut -f1 -d"-");
    
    echo "analyzing...."${nam} 
    
    phyloFlash.pl -lib ${nam} -read1 ${PATH_READS2}/$firstbit-${nam}-QUALITY_PASSED_R1.fastq \
    -read2 ${PATH_READS2}/$firstbit-${nam}-QUALITY_PASSED_R2.fastq -almosteverything -CPUs 10 \
    -readlength 150 -dbhome ${PATH_DB}

    done


# Compare different samples to one another, either in a heatmap
# or a barplot format.
phyloFlash_compare.pl --allzip --task heatmap, barplot

In 2020 Dahle group sent 60 samples for sequencing from various chimneys across the AMOR. The wiki here is to share the pipeline I used to process this dataset. The intent is to be specific about all steps involved, and to provide other lab members with this information so that they do not have to repeat the same time-consuming processes. By using my Git page, there is an added benefit of accountability and having someone to email if something doesn't work for you. :)

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