RNA004 data

[ChaseWLW]

Dear developers, first of all, thanks a ton for this wonderful resource!

With the recent release of the RNA004 kit, do you also plan to make some RNA004 data available in the database?

[cying111]

Hi @ChaseWLW , thanks for showing your interest in the data resource.

Yes, we do have plans to include data generated using the RNA004 kit for future releases. Stay tuned for our data updates that will come soon in the coming months!

You can also sign up for the sg-nex-updates email list to receive notifications about upcoming data releases here.

Thank you Warm Regards, Ying

[haotianteng]

Hi @cying111 I have downloaded your released RNA004 reads for HEK293T cell: SGNex_Hek293T_directRNA_replicate5_run1.pod I have a quick inspection of the data, and here is the returned information for one of the read:

read_id: 0fa7ea06-e289-427f-b256-e19f7203eecb
read_number:	201251
start_sample:	593522006
median_before:	206.00022888183594
channel data:
	channel: 703
	well: 3
	pore_type: not_set
end reason:
	name: signal_positive
	forced: False
calibration:
	offset: -276.0
	scale: 0.1462070643901825
samples:
	sample_count: 147018
	byte_count: 152006
	compression ratio: 0.517
run info:
	acquisition_id: aae2b73c2c106865c1fca563d17a64cc12adeb2c
	acquisition_start_time: 2023-04-10 03:01:45.033000+00:00
	adc_max: 2047
	adc_min: 0
	context_tags: {'barcoding_enabled': '0', 'experiment_duration_set': '4320', 'experiment_type': 'genomic_dna', 'local_basecalling': '0', 'package': 'bream4', 'package_version': '7.4.8', 'sample_frequency': '4000', 'sequencing_kit': 'sqk-rna002'}
	experiment_name: 
	flow_cell_id: PAO51086
	flow_cell_product_code: FLO-PRO002
	protocol_name: RNA004_scripts/RNA004_V1/sequencing_RNA004_V1_Prom:FLO-PRO002:SQK-RNA002
	protocol_run_id: 08baabbd-672c-4fc8-b6b5-089bc197e110
	protocol_start_time: 2023-04-10 02:55:57.844000+00:00
	sample_id: HEK293T
	sample_rate: 4000
	sequencing_kit: sqk-rna002
	sequencer_position: 3A
	sequencer_position_type: promethion
	software: python-pod5-converter
	system_name: PC24A004
	system_type: PRO-PRC024

So it seems the sequencing kit is still shown as "sqk-rna002", I just want to confirm that it's just an error in the meta information and this is the RNA 004 dataset.