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Hello @benjjneb,
I am using R to run dada2 to denoise my 16S rRNA fastq from Ion Torrent PGM. I am wondering whether there is any dada2 tutorial for PGM? Even though dada2 support IT, but all the c…
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Hello,
I'm getting several errors (below) when running joint VC with Strelka2 in bcbio-nextgen v.1.1.3 (stable). HaplotypeCaller works fine on my input data.
It also looks like Platypus isn't be…
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Hi, I'm using DADA2 workflow for Big Data: Paired-end using version 1.8
It worked fine but after constructing seq table I got a message
"The sequences being tabled vary in length."
This is the sum…
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Hi,
I have just installed picrust on Linux. Whenever I try to run the Normalize OTU Table by function part of picrust,
normalize_by_copy_number.py
-i your_otu_table.biom
-o norm…
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Hi Ben,
I am working through the dada2 pipeline for the first time and I found only few sequences can be merged using the function mergePairs, which I chosen the default argument.
here is the re…
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In discussion with @widdowquinn about when any synthetic controls in the reads should be dropped, I think we agreed this ought to be as part of ``thapbi_pict prepare-reads`` (see also #42). i.e. When …
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I am using SeekDeep to extract the reads from some amplicon sequencing. The sequences have already been demultiplexed into a pair of files per sample, and I want to split these into files for each of …
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I am using the 515F 926R primer which targets all three domains of life. A known challenge with this primer set with regards to amplicon sequencing is that the eukaryotic sequences are ~150bp longer t…
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I am working with sina and this is the script which i have used it takes too much time still it is not complete. is it running ok?
(sina) pkd@pkd-HP-406-G1-MT:~$ sina -i ~/Sina/amplicons_seeds.fast…
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Hello !
It has been a while since I used DADA2, and recently updated it directly from version 1.4.0 to 1.9.3. Following the changelog, I understood there were some differences and bug corrections w…
leasi updated
5 years ago