User: benjamin.j.callahan

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Posts by benjamin.j.callahan

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Answer: A: Using DADA2 output for DESeq2
... Performing differential abundance testing is valid at the ASV level, or at the genus level. The optimal choice really depends on your scientific question, and the phylogenetic depth at which the phenotypic traits relevant to that question are conserved. This is anecdotal, but when I am doing differ ...
written 13 months ago by benjamin.j.callahan40
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Comment: C: The ShortRead package does not handle quality score '~' (Q=93) found in PacBio f
... I just tested this in 1.36.1 and am still getting the same behavior (ignoring Q=93) and the underlying code for alphabet still looks the same (aphabet not extended to Q=93). Edit: Nvm, looks good now, just hadn't fully detached the old package version. Thanks again! ...
written 13 months ago by benjamin.j.callahan40
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The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
... I am working with PacBio data in fastq format. The PacBio software outputs fastqs that contain quality scores ranging all the way up to Q=93, encoded as the ASCII 33+93 = `~`. This is causing a problem within the ShortRead package, because the fastq quality score alphabet is hardcoded to extend onl ...
shortread fastq pacbio written 14 months ago by benjamin.j.callahan40 • updated 14 months ago by Martin Morgan ♦♦ 23k

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