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