Does trimming of sequence read alters RNA-Seq gene expression estimates?
We find that aggressive quality-based trimming has a large impact on the apparent makeup of RNA-Seq-based gene expression estimates, and that short reads can have a particularly strong impact. We conclude that implementation of trimming in RNA-Seq analysis workflows warrants caution, and if used, should be used in conjunction with a minimum read length filter to minimize the introduction of unpredictable changes in expression estimates.
Combining EHC and IHC under the term perihilar cholangiocarcinoma is valid, as these tumours have comparable biological behaviour, with similar clinical management depending on stage and invasion.