Comments (5)
With this low coverage I think yacrd can generate some false positive. There is a high chance that a region of the genome is sequenced only once, yacrd can't made difference between this type of read and chimera.
If you have a good reference genome I think map reads on reference is a best way to detect chimera. Alvis should help you, don't trust yacrd result present in publication they made a little mistake
If you have any other question please ask.
from yacrd.
Hi, thank for your interest to yacrd.
As I understand it, out of 1.9m reads, only 454k are NotBad and can therefore be used in further analyses ?
To a first approximation I would say yes.
But it is possible that the recommended parameter is a bit to strict for your data.
Based on your message I guess your data is genomic nanopore R9.4 of rat
What is your coverage? What is your error rate?
from yacrd.
Thanks for that.
Coverage is about 3X, I have another one at about 7X too though.
It's ONT 9.4.1, the accuracy is about 92% from memory.
from yacrd.
Ok it's clearer now, the recommended parameters were determined on datasets with coverage around 30x and 60x, I will add this information in the readme thanks for the bug report.
If you just want detect chimera I think you should run:
minimap2 -x {corresponding preset} {your other parameter} reads.fq reads.fq > overlap.paf
yacrd -i overlap.paf -o reads.yacrd
I don't think run scrubbing reads datasets with such a low coverage rate is a good idea. There is already not enough data for an assembly, reduce information isn't efficient. But if you want to try I think you should lower the minimum coverage to 1 -c 1
.
from yacrd.
Ok, thanks. I'll just do the chimeric read detection. Certainly this was just a Minion test, I won't be performing assemblies on these datasets.
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Related Issues (20)
- Detect fasta or fastq without use extension HOT 1
- Can I use yacrd to remove palindromes in long reads obtained from MDA? HOT 7
- Comparisons with MiniScrub HOT 1
- MDA chimeric reads HOT 3
- Kernel panic at 'called `Option::unwrap()` HOT 2
- Reduce memory usage HOT 1
- escape characters `/` and `\` in ondisk filename HOT 1
- thread 'main' panicked at 'slice index starts at 8092 but ends at 7507' HOT 12
- Error: --input provided more than once.... HOT 2
- yacrd parameters optimization HOT 4
- Filter from .yacrd report HOT 8
- Faster yacrd HOT 5
- Mismatched types HOT 2
- What pipeline should I use? HOT 7
- raw fastq file sequences ID did not fully appear in the *report.yacrd HOT 5
- how about using -X when running minimap2? HOT 1
- Compilation error due to incompatible clap version? HOT 3
- Why the overlap? HOT 2
- Error while running yacrd HOT 6
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