Comments (5)
I think this is the reason why so many of the "interesting" k-mers are in fact inherited from one the parents. I don't think this is an issue of false positive rate.
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No, I'd say it's either a problem with abundance queries (very unlikely) or my new banding approach to counting the k-mers in the first place (much more likely).
from kevlar.
Several issues I've uncovered over the last couple of days.
- The assumption that a k-mer hashes to the same value as its reverse complement is baked into the kevlar code everywhere. This was true for khmer's original hash function, but not for the recent updates to support k > 32 and k-mer banding. This is fixed now in khmer's
refactor/hashing2
branch. - The number of reads reported for each contig uses read IDs as a unique key. Paired reads from the BAM-derived human data have identical IDs, using the bitwise flag to distinguish forward and reverse. And even reads downloaded from the SRA using
fastq-dump
don't include pairing information (/1
and/2
) by default.
These findings don't address all of the concerns we've seen with the results, but they will definitely help cut out some sources of confusion.
from kevlar.
Over the weekend I ran kevlar on 3 E. coli genomes. See https://gist.github.com/standage/05c407ccb2cc13c382e1880a6254ed30. The pipeline reported 1451 novel k-mers associated with 517 contigs. These results need some more inspection, but I noticed immediately that kevlar is still reporting some highly inflated k-mer abundances. One of the reported k-mers CACTATGAAAGTGGGCTTC has a reported of abundance of 15 and 17 in the cases, but has a true abundance of 1 and 0. Note: this time kevlar was not run in banding mode.
from kevlar.
It turns out that my intuition regarding FPR was a bit off. See dib-lab/khmer#1619.
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Related Issues (20)
- Bug with log-space transformation
- Command or script for inspecting ambiguous calls
- MemoryError HOT 3
- Execution failed due to high FPR in case HOT 4
- Failed tests HOT 8
- Dead links to tutorial files HOT 3
- Empty files produced by kevlar split cause crash of kevlar assemble HOT 3
- python 3.6 install - pytest failures - 26 failed, 347 passed (pytest 5.3.5?) HOT 5
- Tutorial: Error on running kevlar filter HOT 9
- Clarification - how to avoid high FPR HOT 3
- kevlar memory error HOT 2
- partition, node error HOT 3
- Controls for simlike HOT 2
- VCF Parsing Issue HOT 1
- Where is kevlar? HOT 3
- How to just get the Kmer?
- Kevlar novel multithreading HOT 2
- count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!! HOT 5
- > 30,000 variants reported from trio-analysis with FPR 0.001? HOT 6
- Is kevlar able to detect duplications/repeat expansions and in general CNV? HOT 1
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