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  • Categories: Genetics | Service Level: Minimal | SW Module: riss_util

    A collection of utility scripts developed by the RISS group at MSI, mainly geared towards next-generation sequence data.

    To load this software in a Linux environment run the command:

    module load riss_util

    Available programs:

    bamflags.pl - count the number of alignments with each bam flag
    
    cleanup - delete all but the most recent pbs .e error and .o output files
    
    convert_casava_18 - convert fastq casava 1.8 sequence headers to casava 1.7
    
    cuffplot.pl - Generate summary plots from cufflinks output
    
    extract_fasta.pl - Given a list of sequence IDs and a fasta file, pull sequences out of the fasta file
    
    extract_fastq.pl - Given a list of sequence IDs and a fastq file, pull sequences out of the fastq file
    
    fasta2tab.pl - Convert a fasta file to a tab-delimited flatfile with two columns: sequence ID and sequence
    
    fasterqc.pl - Combine FastQC images from multiple runs into one image
    
    fastq-species-blast.pl - Given a fastq file, blast a sample of the sequences and count how many hits there are to each species
    
    pe-sync-2-files.pl - Check if the reads in a pair of paired-end fastq files are in the same order (synchronized)
    
    profile.pl - profile the cpu and memory usage of the computer
    
    qme - display queued jobs for the current user
    
    redup.pl - Remove exact duplicate reads from paired-end fastq files
    
    resync.pl - Resynchronize a pair of paired-end fastq files
    
    rgttable.pl - Read in a cuffdiff output file (any read_group_tracking file) and print out a tab-delimited file of RPKM values
    
    risstrim.pl - Trim fastq files using Trimmomatic
    
    tab2fastq.pl - Take a tab-delimited file of sequences (two columns: ID and sequence) and turn it into a FASTA file
    
    tophatplot.pl - Generate summary plots from tophat align_summary.txt output files
    
    tophatstatsPE.pl - Calculate read mapping statistics from a Tophat BAM file (obsolete program)

    Run a progam without supplying any options for usage information. Use perldoc to view extended documentation for perl scripts (scripts ending in .pl). For example: perldoc redup.pl