Samples were taked from three different time points: embryonic (EB), juvenile day2 (D2) or adult (DE). Biological replicates are indicated with different numbers (DE1/DE2, …). Biological replicates were loosely staged in order to screen a broader set of transcriptional states.
The libraries were processed the same as for 2021-12-17_Okinawa_Oik, with the following differences.
The rRNA sequences were regions 5543-3728 and 10911-7289 from contig 153
of an assembly of the O9 genome. The preferred reference sequence for O9
is now OP113806.
The GTF annotation neede to run the quality controls with the RNA-seq pipeline was generated from our GFF reference with the following command:
gffread --force-exons --gene2exon --keep-comments --keep-genes -F -E -T /bucket/LuscombeU/common/Breakpoints/Annotations/OSKA2016v1.9/OSKA2016v1.9.gm.gff