Comments (2)
Hi @Kiliankleemann , thanks for letting us know your doubts.
The naming convention is actually based on our lab sample generation,
- the replicate number "Rep", is named based on the biological replicate that is used, and across ONT protocols, so it might be that, for certain replicates, it's generated using all ONT protocols, but for some replicates, it's only available in some of the ONT protocols, but not all ONT protocols
- similarly for the technical replicate number "Run", this is named based on the technical run, it's also named across ONT protocols, so that's why, you see run number not being continuous within one ONT protocol, but if you check across ONT protocols, then it will be continuous, and it should be complete.
For Illumina matched samples, we just selected three replicates of all replicates generated using ONT protocols for each core cell line, so you might find missing replicates here for short read data.
Please let me if this answers your question.
Also, welcome any suggestion on the naming convention that we currently adopted, and we are happy to discuss more about this.
Thank you
Regards,
Ying
from sg-nex-data.
Hi Ying, thank you for your response.
I am a bit confused still since I downloaded all fastq data and for example in the direct RNAseq for the H9 cells I se run 1 and 2 for all biological replicates, except for replicate 1:
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate1_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate2_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate2_run2
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate3_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate3_run2
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate4_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_H9_directRNA_replicate4_run2
For the Hct116 cells its more patchy:
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate1_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate1_run2
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate1_run3
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run2
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run3
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run4
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run5
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate2_run6
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate3_run1
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate3_run4
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate4_run3
/media/kilian/My Book/ONT_longread_singapore/direct_RNA/raw_data/SGNex_Hct116_directRNA_replicate6_run1
- replicate and run make sense :) no need to change names.
from sg-nex-data.
Related Issues (19)
- Fast5 files HOT 3
- Data Release? HOT 2
- sample_id SGNex_MCF7-EV_directRNA_replicate2_run1 is duplicate HOT 1
- Questions about sequin used HOT 2
- questions about data accessions HOT 1
- Raw data in BLOW5 format HOT 10
- two fastq files were not correctly formated HOT 3
- Sequin spike-in reference HOT 4
- Identification of m6A with the SG-NEx samples HOT 1
- RNA004 data HOT 2
- No download for fastq HOT 2
- fast5 file unable to download now HOT 13
- Possible mixup of Illumina short read data Hct116 and HepG2
- Errors in the augmented annotation GTF file HOT 1
- Are there tissue samples available? HOT 1
- What kits were used for Nanopore library prep? HOT 2
- Number of PCR cycles HOT 2
- Short-read data HOT 3
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from sg-nex-data.