search

GoekeLab / sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
97 stars 24 forks source link

RNA004 data #53

Open ChaseWLW opened 8 months ago

ChaseWLW commented 8 months ago

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 commented 7 months ago

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 commented 1 month ago

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.