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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,
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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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, 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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Hello,
I have a dataset sequenced with Novaseq 6000 with 250PE for 77 libraries and four primers: 12S, COI, ITS and 18S, which gave ~1-6 million paired reads per library, with some lower exceptions…
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Dear @priesgo
While going through the pipeline, I realized that the VCF2FASTA does not masks the regions of low coverage. In amplicon sequencing data, there might be regions deprived of reads. I t…
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Hi
Thanks very much for the shared package.
I have been trying to analyse the data by using it, but got some questions and hope can get some help from your side.
I tried to use either TSS norma…
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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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Dear authors!
Good day to you.
I was wondering how I can use SWAMPy for other pathogens? Which parts of the code should I modify?
I have different reference genomes and primer sets. Is there any …
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I am using samtools and htslib latest version 1.9
- OS - Linux Ubuntu 18.04.03 LTS
- compiler (run `gcc --version` or `clang --version`)
gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0
We are using …