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PavlidisLab / Gemma

Genomics data re-analysis
Apache License 2.0
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Add support for Ion Torrent and ABI sequencing #179

Open ppavlidis opened 2 years ago

ppavlidis commented 2 years ago

It turns out that our default RNA-seq pipeline happily analyzed IonTorrent or ABI data and produces seemingly reasonable data

GSE67124 - iontorrent GSE67122. - ABI (they are from the same group but that's probably not relevant) GSE34272 originates from GPL14980 - ABI Solid

There are more examples.

Keeping that data private for now and marked as unusable to be safe.

We need to check if there are specific processing steps we should be doing besides standard Illumina-like e.g. adapter trimming.

ppavlidis commented 2 years ago

See also thread at https://pavlidis-lab.slack.com/archives/C41KJ0THV/p1628816444038000

ppavlidis commented 2 years ago

AB SOLiD data seems to go through the pipeline just fine. We need to confirm if it's okay.