Miscellaneous 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
RemoveFastaDuplicates | Filter fasta sequences to remove duplicate sequence headers
FilterFastxByIDList | Filter fasta/q sequences based on a list of sequence IDs
FilterSequencesByLength | Filter fasta or fastq sequences based on some maximum sequence length
ProcessFastqWithRandomBarcode | Filter fasta or fastq sequences based on some maximum sequence length
FindAdapter | Determine most likely 3' adapter sequence from fastq reads
RemoveHomopolymerRepeats | Filter fasta or fastq sequences based on sequence composition
MatchPairedEndSequences | Match paired-end fastq sequences based on readID
GTF2Fasta | Extract GTF coordinates from FASTA sequence(s)
Fasta2Fastq | Convert FASTA sequence(s) to FASTQ sequence(s)
Fastq2Fasta | Convert FASTQ sequence(s) to FASTA sequence(s)
Fastx_ReverseComplement | Reverse complement FASTA or FASTQ sequence(s)
ParseTandemOutput | Process X!Tandem MS/MS-spectra alignments and output summary table
CIGAR_2_PWM | Reads SAM alignments and converts the CIGAR strings to a position-weight matrix
ReadCoverage | Reads SAM/BAM alignments to the TRANSCRIPTOME and calculates read coverage consistency
FootprintFrameAnaysis | Analyse ribosome footprint alignments in terms of fidelity to annotated coding frames
PeptideDigest | Enzymatically digest a protein reference