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Hi Jody,
I'm interested in analysing TB amplicon sequencing data with TBProfiler and was wondering if it's suitable for that purpose? Have you considered using amplicon data before and do you have…
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The current amplicon coverage script devised by @dr-david won't work for all sets of primers and corresponding amplicons. The current logic exploits non-overlapping amplicon regions/positions to ident…
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Thanks for developing Strainy!
I'm trying to use amplicon-based Nanopore reads to figure out strain abundances in bacterial samples. The pool has 740 strains and each sample may contain ~10 of them. …
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Hi,
Thank you for developing AmpliconClassifier—it has been an invaluable resource for my research. I have a question regarding the interpretation of results in a specific case.
After running Am…
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I am working on a CRISPR data treated by two sgRNAs and sequenced with targeted sequencing. The distance between the two sgRNA is 3000bp which is much longer than amplicon. The targeted area is the w…
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If the primer pair is oriented with the left primer on the positive strand and right primer negative, the amplicon span should have `Strand.POSITIVE`.
```
GGTCCAGTTCAAGTGCTGGGAGAGCATCCTCCACAAGGTCT…
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### Description of the bug
When COMBINE_DATA() is run (when a sample is repeated) the path does not seem to be staged and the step fails.
I have tested this on both `main` and `inx_id` branches.
…
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Hi everyone,
Thank you for developing this useful tool! I'm currently trying to run amplicon_sorter.py on a large dataset (~6M reads) with 3x random sampling. Here’s the command I’m using:
`pyth…
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Thanks for this nice tool @matdoering
I wonder whether it would be possible to specify the desired amplicon size. In my case, I want to amplify small regions of a bunch of genes (one per gene), bu…
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### Is your feature related to a problem?
the latest dorado basecaller config for r9.4.1 is dna_r9.4.1_e8_sup@v3.6
the available basecallers in current version appear to go up to dna_r9.4.1_e8_sup@v…