Adam Taranto
Adam Taranto
Proposed modules names: teloclip filter teloclip extract teloclip extend
#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...
Add output option for `extract` to yield MAF or MSA of overhang-reads that can be viewed in terminal or externally.
Note: Log total bases extended and bases per contig end. Useful for reporting results.
Option: Output BED file coords for extended sequence segments for review.
Hi Andrew, There is some minimal test data in `tests/data` that you can run through the example code in the readme. In the most basic use case teloclip only requires...
That's pretty much correct. > ### Streaming SAM records from aligner > #Filtering the SAM file using samtools view to exclude specific flags > samtools view -h -F 0x2308 mapped.sam...
For extending the contigs/scaffolds I would do something along these lines: 1) Align the long reads to your assembly and filter for clipped-overhangs. This will give you all possible reads...
Can you share some of the extracted reads from `teloclip-extract` containing the telomeric motif here? You can also paste screenshots from IGV here.
Scaffolds can be validated with Hi-C data, and/or by aligning your long read data back to the scaffolded assembly (after gap-filling). In the later case, you would see a bunch...