Comments (1)
Hi,
You are correct. There is unfortunately a side effect of windowing, if the window boundary happens to fall on an indel region.
There are a couple of options you may try:
- Run Racon twice, either with the same (default) window size, or with a slightly different window size. If your input data has a bias towards insertions or deletions, then your consensus sequence will change in length, and the window boundaries in the second round should be different than in the first round and you can just run it with the same default window size. If your consensus does not vary much in length, try using a slightly larger/smaller window size for the second round.
- Since your target sequences are only ~1000bp in length, you can try to bump up the window size to 1000bp or more, and produce a consensus as a single window. That way you will avoid windowing issues altogether.
Hope this helps,
Best regards,
Ivan.
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Related Issues (20)
- error: empty overlap set! and multiple consusnses sequnces HOT 6
- Issue with some files resulting in "overlap is not transmuted" HOT 3
- unequal length error HOT 1
- Improper HOT 1
- terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format HOT 1
- Segmentation Fault (core dumped) HOT 1
- Output record of fixes HOT 1
- VERY slow performance with fastq.gz files HOT 3
- Racon error: empty overlap set!
- polishing contig with Nanopore Q20 read? HOT 1
- Use cDNA to polish exons
- Racon cannot work with duplucates in paf file HOT 1
- How to generate OVERLAP file? HOT 1
- installation on CentOS 7: 'Could NOT find ZLIB: Found unsuitable version "1.2.7", but required is at least "1.2.8"' HOT 1
- Empty Output (non-memory-related issue) HOT 3
- error: overlap is not transmuted!
- racon: invalid option -- 'L' HOT 3
- error: unequal lengths in sequence and overlap file for sequence 2525deca-ece8-4652-8429-19ca02a0aeca! HOT 1
- Racon gives empty output (fasta file) HOT 5
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