Comments (4)
danshu
commented on August 19, 2024
I noticed that the gaps added during scaffolding are of small sizes. How does Arcs determine the gap size and Is this size reliable?
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warrenlr
commented on August 19, 2024
We are working on a manuscript describing parameters, etc, which should be available on a preprint server within a few weeks. The gap size can not be determined since positional information of reads within their molecule of origin is not known. It is arbitrarily set at 10 bp, but it is a placeholder size, as per your intuition.
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danshu
commented on August 19, 2024
Thanks for your explanation! I will read your manuscript when it is ready.
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shameem356
commented on August 19, 2024
@warrenlr :did you release the manuscript ? If yes, please can you share the link ? We are looking to tune the parameters.
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Related Issues (20)
- About Running ARCS in default mode HOT 3
- GCC version update HOT 1
- arcs-1.2.2: abyss-fixmate-ssq sometimes segfaults HOT 9
- Short read length question: can the tool accept 250? HOT 2
- arcs-long: tiny PE-pairs are produced HOT 3
- Scaffolding Expectations HOT 12
- Running ARCS and ARKS HOT 2
- Parameters for corrected ONT reads HOT 2
- arcs-make in bin HOT 2
- Add optional dependency of pigz HOT 1
- unrecognized option '--fastq' HOT 3
- fastq formatting barcodes in BX tag HOT 8
- ARKS fails to create any links with a highly repetitive input HOT 4
- Parameters for PacBio HiFi data HOT 3
- Can this software use HiC data, or need to use the sequencing technology mentioned in your paper? HOT 1
- `arcs-tigmint` and `arks-tigmint` struggle with input files outside working directory HOT 3
- Incorrect program call? HOT 6
- `arcs-long`/`arks-long` vs `LINKS`? HOT 2
- Understanding specific scaffolding output HOT 4
- tigmint-make 'missing separator' error HOT 8
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