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@khdusenbury, I looked at the [JOSS manuscript submission instructions](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements), and I have the following suggestions to build on…
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Hi,
I'm following the MiSeq SOP to analyze some V4 amplicon data (using the AWS Mothur AMI, version 1.40.4) and running into a weird issue..
After combining my paired end reads I have 3515599 s…
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@torognes Don't panic! I've listed here all uncovered lines that may be reachable with a carefully crafted test. That's too many to deal with at once, but maybe we could try to tackle a couple cases p…
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Hello,
I'm using DADA2 version 1.1.1 and following the DADA2 tutorial with my own fastq files. Everything is running fine until I run mergePairs. I have 20 samples and a few them run with no proble…
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Dear DeepSimulator developers,
I would like to use your tool for simulating nanopore reads, resulting from amplicon sequencing. However, all the reads in pass.fastq have exactly the same errors. Are …
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Hello, I have a follow up question regarding issue #633 :
I have data from two sequencing runs: one run on MiSeq using primers 515F/926R, and the other run on 454 using primers 515F/806R. Samples s…
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Hi,
I'm testing out isONclust with my ONT data and want to verify I'm using the correct command. In the readme, it says to use IsoCon pipeline, but the biorxiv paper says you used isONclust.py.
…
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I have a strange problem - mapping for the bottom strand is not reported even though I can "see" bottom strand reads in the `fastq` file.
**Background**
Got reads generated by Ion Torrent PGM, th…
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Hi,
I am trying to assemble two short, partially overlapping PCR fragments (6.8 kb + 2.2 kb). The fragments have been mixed equimolarly and sequenced on a Nanopore MinION system (LSK109 ligation li…
scogi updated
4 years ago
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**Describe the bug**
A clear and concise description of what the bug is.
Alignment issue - main concern here is probably the amplicon sequence (is it the sgRNA sequence (a.k.a the recognition sequen…