Bunch of tools for RNA and protein analysis
Usage: java -Xmx2G -jar Thunder.jar <Command>
Available <Command> options:
GetSequenceLengths | Get the distribution of sequence lengths in a FASTA/Q file
FastaHeaderGrep | Filter fasta sequences based on the sequence ID
FilterSequencesByLength | Filter fasta or fastq sequences based on some maximum sequence length
RemoveHomopolymerRepeat | Filter fasta or fastq sequences based on sequence composition
MatchPairedEndSequence | Match paired-end fastq sequences based on readID
GTF2Fasta | Extract GTF coordinates from FASTA sequence(s)
ParseTandemOutput | Process X!Tandem MS/MS-spectra alignments and output summary table
CIGAR_2_PW | Reads SAM alignments and converts the CIGAR strings to a position-weight matrix