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# Request a 180 minute interactive node on the normal queue using today'sour reservation
idev -m 120 -N 1 -A OTH21164 -r CoreNGS-Wed
idev -m 120 -N 1 -A TRA23004 -r CoreNGS

# Request a 120 minute idev node on the development queue 
idev -m 120 -N 1 -A OTH21164 -p development
idev -m 120 -N 1 -A TRA23004 -p development

# Using today'sour reservation
sbatch --reseservation=CoreNGS-Wed <batch_file>.slurm

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# Load the main BioContainers module then load the fastqc module
module load biocontainers  # make take a while
module load fastqc

It has a number of options (see fastqc --help | more) but can be run very simply with just a FASTQ file as its argument.

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idev -m 120 -N 1 -A OTH21164 -r CoreNGS-Wed      # or -A TRA23004 
idev -m 120 -N 1 -A OTH21164 -p development  # or -A TRA23004

FASTX Toolkit is available as a BioContainers module.

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Because the [-i INFILE] [-o OUTFILE] options are shown in brackets [ ], reading from a file and writing to a file are optional. That means that by default the program reads its input data from standard input and writes trimmed sequences to standard output:

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• The -l 50 option says that base 50 should be the last base (i.e., trim down to 50 bases)
• The -Q 33 option specifies how base Qualities on the 4th line of each FASTQ entry are encoded.
  
  • The FASTX Toolkit is an older program written in the time when Illumina base qualities were encoded differently, so its default does not work for modern FASTQ files.
  • These days Illumina base qualities follow the Sanger FASTQ standard (Phred score + 33 to make an ASCII character).

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idev -m 120 -N 1 -A OTH21164 -r CoreNGS-Wed      # or -A TRA23004 
idev -m 120 -N 1 -A OTH21164 -p development  # or -A TRA23004

module load biocontainers
module spider cutadapt 

module load cutadapt 
cutadapt --help | more
cutadapt --help | less

A common application of cutadapt is to remove adapter contamination from RNA library sequence data. Here we'll show that for some small RNA libraries sequenced by GSAF, using their documented small RNA library adapters.

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echo $(( `zcat Sample_H54_miRNA_L004_R1.cat.fastq.gz | wc -l` / 4 ))
# or
zcat Sample_H54_miRNA_L004_R1.cat.fastq.gz | wc -l | awk '{print $1 / 4}'

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