Figure: NanoStats

• create a figure/table for the NanoStats output

changed milestone to %Manuscript - initial version

added Figure label

I assume the data is in *NanoStats.txt files?

find /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling -type f -name "*NanoStats.txt"

Found files in /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/:

2019_GDB/results/qc/lr/S3_Gtube/no_barcode/no_barcodeNanoStats.txt
2019_GDB/results/qc/lr/S3_Gtube/unclassified/unclassifiedNanoStats.txt
2019_GDB/results/qc/lr/merged/no_barcode/no_barcodeNanoStats.txt
2019_GDB/results/qc/lr/merged/unclassified/unclassifiedNanoStats.txt
2019_GDB/results/qc/lr/S1_SizeSelected/no_barcode/no_barcodeNanoStats.txt
2019_GDB/results/qc/lr/S1_SizeSelected/unclassified/unclassifiedNanoStats.txt
2019_GDB/non_methylation_aware_results/qc/lr/S3_Gtube/no_barcode/no_barcodeNanoStats.txt
2019_GDB/non_methylation_aware_results/qc/lr/merged/no_barcode/no_barcodeNanoStats.txt
2019_GDB/non_methylation_aware_results/qc/lr/S1_SizeSelected/no_barcode/no_barcodeNanoStats.txt
results/qc/lr/merged/barcode07/barcode07NanoStats.txt
results/qc/lr/20181107_0906_same/barcode07/barcode07NanoStats.txt
results/qc/lr/20181108_0827_test/barcode07/barcode07NanoStats.txt
results/qc/lr/20181106_1450_noselection_sizeselection/barcode07/barcode07NanoStats.txt
non_mod_basecalled_results/qc/lr/merged/barcode07/barcode07NanoStats.txt
non_mod_basecalled_results/qc/lr/20181107_0906_same/barcode07/barcode07NanoStats.txt
non_mod_basecalled_results/qc/lr/20181108_0827_test/barcode07/barcode07NanoStats.txt
non_mod_basecalled_results/qc/lr/20181106_1450_noselection_sizeselection/barcode07/barcode07NanoStats.txt

For the methylation aware basecalling:

2019_GDB/results/qc/lr/S3_Gtube/no_barcode/no_barcodeNanoStats.txt
2019_GDB/results/qc/lr/S1_SizeSelected/no_barcode/no_barcodeNanoStats.txt
2019_GDB/results/qc/lr/merged/no_barcode/no_barcodeNanoStats.txt
# not sure if want the "merged" though

For the non-methylation-aware:

2019_GDB/non_methylation_aware_results/qc/lr/S3_Gtube/no_barcode/no_barcodeNanoStats.txt
2019_GDB/non_methylation_aware_results/qc/lr/merged/no_barcode/no_barcodeNanoStats.txt
2019_GDB/non_methylation_aware_results/qc/lr/S1_SizeSelected/no_barcode/no_barcodeNanoStats.txt

First version: fig_nanostats.pdf

Feel free to comment. I am not sure where the focus should be: comparing the selection methods or methylation/non-methylation aware approach approaches.

I think the merged is the only one of real concern, since we used that for downstream analyses. The other two options were Rashi trying something out. Ideally, this will not be the case.

Maybe (to be confirmed by @cedric.laczny) we will not even need to show the size_selected or gtube selection. This can introduce unnecessary scrutiny. In the methods, we can lay out that we used both methods to capture the variability (or some hand-waving), but my opinion is that it doesn't need to be in the figure itself. What say?

Okay, let's see what @cedric.laczny has to say.

Having said all that.. Nice work @valentina.galata!!

• these are uncharted territories for, dare I say, all of us ;)

Thank you :)

mentioned in commit bc7c5db7

Nice plots @valentina.galata, thx!

I think that this is something we could definitively report. Yes, it might open us up for questions, but, then again, we could immediately try to argue over that by saying that we tested both approaches and used them together to have "longer" and "shorter" reads in the assembly. Then again, one might question if this has added any benefit

Too many variables, but let's just go with it and deal with it then, I guess!

So, should I include only merged or keep the plot as it is?

• Sorry that discussion was inconclusive, like everything in Science..
• please keep it as-is

Okay, keeping the plot as is. Feel free to re-open the issue if something should be changed.

closed

mentioned in commit 629dc3fc

changed title from figure-request-4: Nanostats to Figure: Nanostats

changed title from Figure: Nanostats to Figure: NanoStats