Gene Count Table Requirements Missing

[vccri]

Gene Count Table Requirements Missing

[davhum]

Sorry for delayed reply.

Short answer: The gene count file is not used for a lot of the core functionality of Ularcirc- rather some of the QC plots (eg PCA) where BSJ are normalised against a CPM. The most important files are the FSJ and BSJ files. So perhaps in this instance you might consider not uploading the gene count file.

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Gene count table format::

Ularcirc only accepts gene counts in format as generated by STAR aligner. i.e:

gene name \t unstranded \t Forward strand counts \t Reverse strand counts

unstranded counts should equal forward strand + reverse strand (but this is not checked)

Most illumina libraries will generated counts to negative strand (i.e. opposite strand of gene model). I see that the RSEM does not generate a raw count output which is what Ularcirc expects. Ularcirc calculate a CPM from raw counts to normalisation BSJ counts. If you pass the RSEM TPM or FPKM values then ularcirc will incorrectly generate a CPM. However this will only affect PCA plots that are generated on a CPM option.

[davhum]

I am closing this issue now, but am happy to discuss other functionality that could be used with the gene count file.