add support for gzipped BED/text files across all tools
Closed this issue · 1 comments
owlang commented
As we work with increasingly large input BED/GFF coordinate files in our analysis, support for gzipped input becomes increasingly important for efficient and optimized use of computing resources. Ultimately all tools that use any flat text input file format should support their gzipped versions (BED, GFF, TAB, FASTA, FASTQ).
- Prioritize TagPileup
- Add a GUI tool for gzipping and unzipping files
- Modify FileSelector to include file filters that allow for both the regular (unzipped extensions) and their gzipped counterparts
- Move through rest of tools...
owlang commented
Tools with BED input/output...
Read_Analysis
- Aggregate Data
- TagPileup (v0.14)
- Scale Matrix
- Scaling Factor
- Similarity Matrix
Coordinate Manipulation
- ExpandBED/GFF (v0.14)
- Sort BED/GFF
- BED-to-GFF
- GFF-to-BED
- Shift BED/GFF (v0.14)
Sequence Analysis
- DNA-shape-from-BED
- DNA-shape-from-FASTA
- FASTA extract
- Randomize FASTA
- Search Motif
Peak Analysis
- Peak Align to Ref
- Filter Peak by Proximity
- Tile Genome
- Random Coordinate
- Signal Duplication
Figure Generation
- Two Color Heatmap (v0.14)
- Three Color Heatmap (v0.14)
- Four Color Sequence
- Label Heatmap
- Merge Heatmap
- Plot Composite
BAM Format Converter (Output GZip)
- BAM to BED
- BAM to GFF
- BAM to BedGraph
- BAM to ScIdx
Peak Calling
- Gene Track
- Peak Pair
File Utilities
- Convert Chr Names
- Compress File
- Decompress File
- MD5 Checksum
BAM Statistics
- N/A on all tools
BAM Manipulation
- N/A on all tools