Demultiplex custom barcode

[Seongmin-Jang-1165]

Issue Report

Please describe the issue:

hello. i want to demultiplex direct RNA seq data(POD5 format).

i referenced the description "Custom Barcode Arrangements", but ther error is occured. i attach the error message. what is the problem of my code or something else..?

[arrangement]
name = "custom_barcode"
kit = ""

mask1_front = ""
mask1_rear = ""
mask2_front = ""
mask2_rear = ""

Barcode sequences

barcode1_pattern = "BC_C%02i"
barcode2_pattern = "BC_M3%02i"
first_index = 1
last_index = 2
rear_only_barcodes = true

Scoring options

[scoring]
max_barcode_penalty = 11
barcode_end_proximity = 75
min_barcode_penalty_dist = 3
min_separation_only_dist = 6
flank_left_pad = 5
flank_right_pad = 10
front_barcode_window = 175
rear_barcode_window = 175
midstrand_flank_score = 0.95

barcode_fastq

BC01
GTACTTTTCTCTTTGCGCGG
BC02
GTGATTCTCGTCTTTCTGCG

[Seongmin-Jang-1165]

i used SQK-RNA004 library kit and barcoding with 2 specific-adapter

[malton-ont]

Hi @Seongmin-Jang-1165,

The parser is saying you have an error in the line name = "custom_barcode". There doesn't seem to be an error present in what you've pasted here, so please check the original file.

You also have some other issues:

• Your fasta file does not appear to be valid - identifier lines should begin with a >
• Your barcode1_pattern does not match the identifiers in your fasta
• You specify barcode1_pattern and barcode2_pattern, but also rear_only_barcodes - if you only have rear barcodes then there can be no barcode2_pattern
• A custom barcode arrangement must specify at least one of mask1_front or mask2_front - it looks like you're trying to sidestep this to perform adapter detection instead of barcodes? Dorado does not support this.

[Seongmin-Jang-1165]

hi @malton-ont

thank for your advice! it helps me a lot

i prepare library with target-specific adapter and put the barcode sequence into adapter. so it seems like detecting adapter...