Comments (5)
Proposed modules names:
teloclip filter
teloclip extract
teloclip extend
from teloclip.
#10 requests automation of the contig extension process. I think it is generally unwise to blindly accept overhang alignments are "real" without inspecting them first.
Need to balance convenience vs enabling errors.
Could provide tutorial on manual curation: Select the best overhang-read (i.e. confident anchor region, unique alignment, many reads agree) and then extend contig with teloclip extend
.
Alternatively, could provide an extend-now-ask-questions-later option whereby we extend contigs using the longest available overhang and then suggest validation checks i.e. align all overhang-reads back to the extended contig and look for agreement between reads.
from teloclip.
Add output option for extract
to yield MAF or MSA of overhang-reads that can be viewed in terminal or externally.
from teloclip.
Note: Log total bases extended and bases per contig end. Useful for reporting results.
from teloclip.
Option: Output BED file coords for extended sequence segments for review.
from teloclip.
Related Issues (20)
- Automatically extend contigs HOT 1
- error "invalid mode: 'rU' " in teloclip (v. bioconda)
- Refresh codebase
- Automate testing HOT 1
- Package Distribution HOT 1
- No 'rU' option in Python 3.12 HOT 4
- Improve readability
- Confusing about input and output file HOT 17
- Feature: Fuzzy motif search
- Add metadata to extracted overhang reads HOT 1
- Missing isMotifInClip()
- Could you explain in detail how to extend reads? HOT 3
- Calculate alignment end position from CIGAR HOT 1
- Verify: Correct read slice coords for negative strand alignments HOT 2
- Summary report option
- Interactive Contig extension HOT 1
- functionality to extract reads at NNN gaps in scaffolds? HOT 2
- NNNNN reads HOT 8
- Find existing telo repeats in contigs HOT 1
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