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hanyue36 / nanoplexer

Tool for demultiplexing Nanopore barcode sequence data
MIT License
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minimum alignment score options ignored #10

Closed good-ligations closed 2 years ago

good-ligations commented 2 years ago

It seems that the "-s" option for the alignment score is unused or I may be entering it incorrectly. I have tried multiple rounds with varying "s" scores above the default of "22", and the alignment score values are not changed in the log or in the amount of demultiplexed samples.

Command: $ ./nanoplexer/nanoplexer -b ./barcodes.fa -d sample.txt -s 40 -p ./output -l log ../FAO23974_pass_ced4ad01_125.fastq

stdout: 2022-02-07 13:57:02 Minimal alignment score is 22 2022-02-07 13:57:04 Finished demultiplexing sequence data.

$ head log: 0f900e08-52dd-4cb7-a5df-4ec45b9464ef REVERSE10 + 42 H_REV + 42 1e1e0c4c-21cf-41d6-af1c-d63bd591d8ea REVERSE01 + 33 A_REV + 29 19be82b8-1094-4b90-8cf5-1db5d045f484 REVERSE02 + 42 E_REV + 42 c8a67fd7-29d2-4374-b4ab-3243d4647ffe REVERSE03 + 31 A_REV + 42 4de7e4c5-e8e2-4ee0-8a0c-708ad3a7a31b REVERSE01 + 42 F_REV + 42 069fd321-f80c-4cb1-91c1-1e7196597bcf H + 42 REVERSE08_REV + 32 e6df5bca-c01f-402f-9f6c-f3837786a1b0 E + 42 REVERSE03_REV + 34 aa3a79b1-1691-4350-bc51-362188635966 REVERSE02 + 32 E_REV + 42 20161ea4-e32a-4da1-bafa-63e4602202fe REVERSE01 + 28 D_REV + 38 c461726f-5090-4c11-94f8-3ce608865f4d REVERSE01 + 42 F_REV + 42

hanyue36 commented 2 years ago

If you want to specify minimal alignment score, use -i and -s simultaneously.

good-ligations commented 2 years ago

Thank you that worked perfectly! This program works very well for Nanopore datasets!

Are there any options to trim all bases upstream of the forward barcode and downstream of the reverse?

Thank you!

hanyue36 commented 2 years ago

I didn't design the trim option and the barcode sequences should be shown as soft clipping in cigar flag after alignment. I think it doesn't affect downstream analysis. I'll consider to add the option in further version.