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Dear Yichao,
Thanks for sharing your repo with that much useful data/scripts! :)
Would you by chance also have the raw-data of your the .csv files stored under
`https://github.com/YichaoOU/easy_…
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### Description of the bug
Dear authors,
We were trying to use the ampliseq pipeline in sidle mode but get stuck at the NFCORE_AMPLISEQ:AMPLISEQ:SIDLE_WF:SIDLE_DBEXTRACT step.
Looking at the `…
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We have examples where there is a choice of two primers for the end of a given amplicon. Only one primer of the two primers has support from the reads.
Observed behaviour: Both primers are kept, in…
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Hi Diener,
would it possible to provide detailed description on the procedures that generated those GEM reference database? I found it quite useful while I am hesitating to use it in my manuscript wi…
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hi，how to resolve this problem ？
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Writing to output...
Primers combination number 1
Number of written amplicons: 272
Sorting amplicons to multiplexes 1_2 (…
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Is there anything in the structure of amptk that would prohibit using Nanopore amplicon data as input?
Fragment lengths are ~1500 bp. Input fastq are already adapter and quality trimmed and demulti…
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+ Quantify against CDS seqeunces
+ reasoning: microbes express polycistronic transcripts, but genomic rearrangements and other biology between strains makes it hard to have good references at the…
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I have a multiplex run composed of 20 different barcode libraries with all libraries having the same amplicon fragment (same 1st PCR with all the same primers). The sequencing provider sent me the dem…
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At one locus in this dataset I see that iVar is soft-clipping all the bases except 1 when that base is next to an insertion and mismatches the reference.
I've also included illumina data from the sam…
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Hi Author(s),
I think it is super cool that you've implemented this dynamic strategy!
We where trying to normalize some amplicons on a given chromosome, so we made sequences that where unique to…