Is it possible to consider primer reads during demultiplexing? about nanomux

[willros]

Hi,

Thank you for your comments!

1. I will add the option to not remove the barcodes.

2. It is because you have choosen to have 4 mismatches in fuzzy mode. I will put a cap at 1 or 2 I think, because otherwise this will happen. How long barcodes do you have?

3. Nice to know! I will make the program work in batches instead for reading everything into memory at once!

I'll let you know when I am done!

Thanks!
William

[Jia-Xiu]

Thanks for considering these options!

I will try to set a cap of 1 or 2 as you suggested and check the results. My barcodes are 24nt long.

How about incorporating barcodes with degenerate bases? For example, using Y to represent A or G, and R to represent C or T.

Thanks!
Xiu

[willros]

I will try.

Please try it with greedy mode as well and check the results!

[willros]

I have now added the three points that you suggested. Thanks for the nice suggestions!

Please reinstall everything and try it out! See the new readme for usage.

Regards,
William

[willros]

Hi @Jia-Xiu,

I did a lot of changes to the fuzzy searching algorithm now.

Mismatch of 3 works good for me now. It is quite much slower than if using 1 or 2, but it finds more barcodes and not as many duplicates as before.

Please download the newest version and try again!

Thanks,
Ville

[Jia-Xiu]

Thank you @willros!

My job using the previous version is still running. It takes about 2 hrs to write the output of each sample (fuzzy with mismatch of 1). I will run the new version and check the results.

Cheers,
Xiu

[willros]

Maybe kill the current job and try again with the newest version.

How many samples do you have to demux?