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rje_genomics V0.9.0Genomics data reformatting module
Copyright © 2018 Richard J. Edwards - See source code for GNU License Notice Imported modules:
See SLiMSuite Blog for further documentation. See FunctionThe function of this module will be added here. reformat: convert TDT file into GFF or SAM ncbi: combine NCBI accession numbers and annotation with local data gffmap: convert GFF files from one ID set to another samfilt: filter read alignments from SAM file mapbam: map a set of IDs from a BAM file and output an updated SAM file CommandlineGeneral Options
Reformat Input/Output Options
NCBI Annotation Options
NCBINR Protein filtering Options
GFF Map Options
FASTQ Options
GAP GFF Options
SAM Filter Options
BAM Mapping Options
History Module Version History# 0.0.0 - Initial Compilation. # 0.1.0 - Added ncbi annotation reformatting. # 0.2.0 - Added diphap renaming of pseduodiploid assembly sequences. # 0.3.0 - Added fqreads counting of reads from fastq.gz. # 0.4.0 - Added GFFMap function for mapping IDs onto others in GFF files. And mapfas mode to make mapping table. # 0.5.0 - Added Fas2Bed function for making a BED file of all contigs for bedtools coverage etc. # 0.6.0 - Added GapGFF option to generate GFF of assembly gaps. # 0.6.1 - Fixed TDTKeys bug. # 0.7.0 - Added loc2gff mode for converting local hits table to GFF3 output. # 0.8.0 - Added samfilt: filter read alignments from SAM file # 0.8.1 - Fixed gapgff bug that had first gap in header. # 0.9.0 - Added mapbam: map a set of IDs from a BAM file and output an updated SAM file rje_genomics REST Output formatsRun with&rest=help for general options. Run with &rest=full to get full server output as text or &rest=format for more user-friendly formatted output. Individual outputs can be identified/parsed using &rest=OUTFMT .© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au. |