Questions
csw edited this page Jul 10, 2012
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13 revisions
Outstanding questions about MAF and MAF workflows:
- Is it useful to build indexes on other sequences besides the reference sequence?
- Should the
scorefield of an alignment block be zeroed or removed whenever the block is modified? - How, precisely, should selection based on features in GTF/GFF3 files work?
- When converting a MAF Block/Sequence to bio-alignment representation, how should we handle quality metadata (from 'q' lines), which is tied to the actual sequence data and would need to be maintained in parallel if a column were deleted?
- Is supporting the bx-python index format still desirable? Performance with Kyoto Cabinet indexes seems competitive, and the indexes are neither very large nor very expensive to build.
- Blankenberg et al. mention this filtering mode: "removing blocks which have aligned species occurring between non-syntenic chromosomes or strands" which is unfortunately a bit cryptic.
- Are coverage statistics useful or appropriate to provide?