Misspecification gtf in STAR_outline MWE of RNA_calling,

[hsun3163]

Originally, to generate the STAR_Index and RSEM_index, the same gtf, the gtf prior to collapse by gene should be used. However, as we decided to do STAR_indexing on the fly, it slip my mind and gave a wrong example in the RNA_calling pipeline test MWE reference_data/Homo_sapiens.GRCh38.103.chr.reformated.ERCC.gene.gtf.

Therefore, all the Aligned.toTranscript.bam that were generated by Traves and Shrithee can not be used to conduct RSEM analysis.

Luckily, the main expression matrix we used is the one from rnaseqc, based on the Aligned.byCoordinated.bam, which should not be impacted by the gene vs transcriptome.

To fix it, STAR_align (Not the star_output since that will overwrite the existing md.bam which will take double the time) needs to be rerun to regenerate the Aligned.toTranscript.bam file (edited)

The consequence is that the RSEM bed table will not be generated on time