• C.elegans data (Pubmed):Includes supplemental data from Ganko et al 2003 and up-to-date Wormbase Browser retrotransposon location files
  • LTR_STRUC (Pubmed): Application from McCarthy and McDonald 2003 that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits

Other sequencing data analysis programs from our lab:

Program Description
CountSplicedReads Counts the number of spliced reads (or splice junction mapping reads) in a given RNA-Seq reads genomic alignment bam file.
DetermineFastqQualityEncoding Determines quality value encoding format in a given fastq file.
FastqPairedEndValidator Validates order of paired-end reads in given fastq files.
AddPairedEndSuffix Adds \1 and \2 suffix (tags) to the first (left) and second (right) pairs of paired-end read names respectively in given fastq files.
FqToSamPicard Converts paired-end fastq files to a merged and sorted (on read name) SAM file.
UnmappedSamToFastq Fixes the order of appearance of paired-end reads in fastq files using a merged SAM files and also separates unpaired reads.

Other resources:

    • How to fix the order of appearance of mates of paired-end sequencing reads in fastq files?
    • How to improve RNA-Seq alignment using TopHat? (2013)
    • Evidence and potential clinical significance of changes in gene network interactions in ovarian cancer – Christopher G. Hill, John F. McDonald