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Hello,
I am trying to run the ARTIC pipeline on the Singularity profile with the new ARTIC V4 primer scheme set (https://github.com/artic-network/primer-schemes).
I am running the Nextflow pipeli…
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This lesson is meant to be a bit modular, so that it can be adapted to a few different workflows depending on user preference. That said, we do need a default one. Here are my thoughts:
**OTUs vs. …
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Hi there,
I'm very excited to try using `decontam`, but I'm not sure it'll work with our data. I'd be grateful for any advice.
I've got the following `phyloseq` object (16 true samples and 5 con…
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We have been using 60GB of ram for ABRA2 on deeply-sequenced bams (20,000x total, 1,200x unique, ~10 GB in compressed size).
We would like to be able to realign as many bams together as possible, …
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Hi all,
We are sequencing minION flowcells using the ARTIC amplicons and beginning to test out the ARTIC workflow as described on this page:
[ARTIC SOP 2019](https://artic.network/ncov-2019/ncov…
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Hi,
I was hoping someone could give some insight into this problem I am having.
For my amplicon duplex reads (length ~ 1.2kb) I find that some basecall in duplex excellently using the latest Dor…
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Hi, I reanalysed my Illumina miseq data and found some discrepancies between the old and my new results. I will post my code and the R output here in the hope of receiving some feedback on the accurac…
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When we use STAR to map the results of targeted sequencing we merge the gencode annotation with specific amplicons we use for targeted amplification. (We design primers close to polyA site in the 3-pr…
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From Allison Heath and Eric Wenger:
Good morning, quick question on what the Ontology WG recommends for c2m2 OBI id's in several cases where we are not seeing matches.
Kids First data has several…
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Can the `fastx_getseqs` be included too? Seems it has been removed compared to version 11:
`Unknown command-line option -fastx_getseqs`