Known Issues
Human H1_mix
- Replicate 3 of the H1_mix sample appears to be an outlier among the CapTrap ONT library type. This was identified by looking at concordance between expected 5’ and 3’ adapter sequences and the strandedness (directionality) of minimap2-aligned spliced reads by looking at splice site sequences.
- Replicate 3 of the H1 mix has two paired-end fastq files for the Illumina library type. These should be combined in analyses, as they come from the same mix of biosamples.
Manatee
- Percentage of sequenced spike-in SIRVs is higher than expected. For example, the PacBio library has 14% of reads corresponding to SIRVs
- The ONT cDNA and PacBio cDNA data from size selected and non-size selected libraries that should be combined and included in the submission. It is up to the submitter how they decide to combine the information, e.g. just merge the reads or treat size-selected and non-size selected differently during the processing.
R2C2 libraries
- It was intended to keep size-selected and non-size-selected R2C2 libraries in separate files; however, they should be combined for analyses, which has caused confusion. The data for each bioreplicate should be combined for both Challenges 1 and 2.