Comments (3)
the input trace qualities are not very useful
This piqued my interest, would you mind expanding on it a bit? In my department, one of the concerns I come across as a proponent of tracy is the lack of informative quality scoring and the fact that Ns appear in our sequences at a very very low rate compared to other basecalling algorithms - combined, these attributes make my colleagues cautious.
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The quality scoring is indeed a bit of an issue because the input trace qualities are not very useful. The assemble command simply scales a flat quality prior by the fraction of traces supporting the consensus nucleotide. For 2 input traces, it is thus indeed only 1 or 2 traces supporting the consensus nucleotide. For more input traces, you should see a range of quality values.
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OK thanks - that's interesting. I'm using Tracy to detect errors in sequencing data, which can range from 1 trace (where I use basecall
) to 4 traces (assemble
).
As per your explanation, this sounds like forming a consensus between 2 traces for a given nucleotide doesn't consider the quality of the base call, and rather just looks at the fraction of traces involved in generating the consensus.
Below summarises my understanding for 4 different base quality configurations for the assembly of 2 trace files - is this accurate? To my mind, the 3rd and 4th scenarios should have lower quality values than the 1st.
Part of the problem for me is that I want to have some estimate of the per-base quality score, so that I can confidently calculate the per-base error rate. In practice, this is hard using tracy
because the quality scores change depending on how many trace files I use, and don't seem too comparable between a 2-trace assembly and a 4-trace assembly.
Is there a workaround?
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Related Issues (20)
- SCF version greater 2.9 required! HOT 4
- Only single-chromosome FASTA files are supported HOT 1
- Can tracy assemble trim option be disabled? HOT 1
- Decompose doesn't give bcf file give json instead HOT 3
- Base quality and consensus generation HOT 7
- How can I provide a file with a list of input files to tracy? HOT 2
- Indigo HOT 4
- Cannot execute Tracy binary on mac HOT 5
- Bioconda tracy package runs very slowly where precompiled binary is fast HOT 2
- terminate called while attempting to run tracy on WSL HOT 1
- [feature request] Further options to control trimming with consensus HOT 5
- -p signal to noise ratio HOT 1
- Annotation error in the results generated sanger sequencer HOT 4
- `Couldn't anchor the Sanger trace in the selected reference genome.` error in tracy but not in Indigo HOT 3
- Issues Installing/Compiling on Mac HOT 2
- docker images differences between quay.io and dockerhub HOT 4
- Options for specifying overlap, 'fracmatch' in consensus subcommand
- Can tracy's consensus option be updated?
- Hemizygous calls HOT 2
- basecall problem HOT 2
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