https://github.com/gersteinlab/thunder

Rob's random collection of mostly RNA-seq tools
https://github.com/gersteinlab/thunder

Last synced: 2 months ago
JSON representation

Rob's random collection of mostly RNA-seq tools

• Host: GitHub
• URL: https://github.com/gersteinlab/thunder
• Owner: gersteinlab
• Created: 2015-07-16T13:12:06.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2016-06-16T17:58:28.000Z (almost 9 years ago)
• Last Synced: 2025-01-20T12:07:42.526Z (4 months ago)
• Language: Java
• Homepage:
• Size: 11 MB
• Stars: 1
• Watchers: 22
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# Thunder

Bunch of tools for RNA and protein analysis

Usage:	 java -Xmx2G -jar Thunder.jar \

Available \ 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