Conflict with header format of Seurat FindAllMarkers

bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data

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Conflict with header format of Seurat FindAllMarkers #18

Closed olgabaranov closed 3 years ago

olgabaranov commented 3 years ago

The current version of Seurat (v4) seems to export the table naming the log fold change column 'avg_log2FC' while the script expects 'avg_logFC'. It can be fixed by changing the line 370 of the script to fit the new format

bioinfo-ibms-pumc commented 3 years ago

Thanks for the suggestion. You have got the right solution. Because it's hard to adapt to all the headers generated by various software, so you may fixed the problem by changing either the script or the title in the current version. I don't know whether it is worth to develop a converter for the data structure yet. But thanks for reminding.