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I would like to use LACA for shorter amplicons (600 bp) from ONT sequencing.
Can you provide the following options in the laca init so that the config file can work with alternative sequence input…
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We have examples where there is an amplicon with two right-hand primers. Neither primer is excluded at the primer/amplicon identification stage, and both are provided to cylon.
Observed behaviour: …
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**Describe the bug**
CRISPResso version 2.2.14
[Command used]:
/home/albustruong/miniconda3/envs/ngs/bin/CRISPResso -r1 2404-1-A4.R1.clean.fastq -r2 2404-1-A4.R2.clean.fastq --amplicon_seq ATTGCAGA…
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Hi,
I would like to analyse multiple samples at once after demultiplexing. As input data I have one fasta file for each sample and each amplicon.
I'm not sure how to organise my data and I coul…
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When providing a target fasta longer (e.g., 1kb) than the specified amplicon (250 nt), the histogram PDF appears to calculate median mutation rate incorrectly (specifically, deflates the mutation rate…
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In the AmpliconClassifier documentation is detailed, that only cyclic amplicons can be classified into BFB or ecDNAs.
However, in my analysis, I noticed that some were classified as Complex, but the…
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I belately saw this message from @BioWilko https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473/17
>Hi, in regards to our [post about erroneous mutations in ARTIC V4/4.1 3](https://…
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Thanks again for this great tool (creating a separate issue for a very different question)!
I have a question about alignment behavior in CRISPResso. My understanding was that the software was agno…
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Hi,
I am attempting to run your code on targeted sequencing data from an S5 instrument that has probes across multiple chromosomes. For your probe information file there are required sections for G…
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# Possible reasons for duplex reads' quality are low
Hello, thank you for increasing the read quality! We always observe higher read mean quality on duplex than simplex reads, especially simplex pa…