BC01 empty

[AhmedAbdelfattah]

Hi all,

I am running jsa.np.barcode with an input of about 4 million reads. The -bc is fasta file containing ONT barcodes from thier barcoding kit:

BC01
AAGAAAGTTGTCGGTGTCTTTGTG
BC02
TCGATTCCGTTTGTAGTCGTCTGT
BC03
GAGTCTTGTGTCCCAGTTACCAGG
BC04
TTCGGATTCTATCGTGTTTCCCTA
BC05
CTTGTCCAGGGTTTGTGTAACCTT
BC06
TTCTCGCAAAGGCAGAAAGTAGTC
BC07
GTGTTACCGTGGGAATGAATCCTT
BC08
TTCAGGGAACAAACCAAGTTACGT
BC09
AACTAGGCACAGCGAGTCTTGGTT
BC10
AAGCGTTGAAACCTTTGTCCTCTC
BC11
GTTTCATCTATCGGAGGGAATGGA
BC12
CAGGTAGAAAGAAGCAGAATCGGA

The script is running fine, but I just noticed that BC01 is an empty file. I have already demultiplexed this data set with Metrichor, when it was active and I know that I have sequences with BC01.

Is there a reason this could happen?

[hsnguyen]

Hi Ahmed,
Thank you for your interest in our work.
jsa.np.barcode had originally been created for our own experiment and BC01 omitting was one of our settings before. But yes, it surely doesn't fit to the other use-case. You can find it fixed by pulling the newest commit of japsa and reinstall.

This module, although being useful for streaming analysis, yet has limited usage for inexperienced user. For that reason, we're trying to integrate it into jsa.np.npreader so that the demultiplexing can be established in a real-time fashion with the basecalling (just like Metrichor). Despite more tests are ongoing, we can say that it's very near to be released.
From newest git commit of Japsa, please try jsa.np.npreader -GUI to run on your base-called data and give us more feedback. Thank you!