Comments (1)
mbelmadani
commented on June 18, 2024
The current "best" way to do this is to create custom transcriptomes with the appended ERCC sequences and annotations to the fasta/gtf files respectively.
Then a configuration mode must be specified so that the $QUANTDIR is set to the $ERCCDIR and the reference pointed to the ERCC transcriptome (example: https://github.com/PavlidisLab/rnaseq-pipeline/blob/master/etc/modes/mouseERCC.cfg).
Then the user simply can launch the jobs with the xxxxERCC mode set.
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Related Issues (20)
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