Search Software

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

SW Documentation: 

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

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