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add barcoding info to the sequencing summary when turned on #44

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Psy-Fer opened this issue Aug 20, 2024 · 1 comment
Closed

add barcoding info to the sequencing summary when turned on #44

Psy-Fer opened this issue Aug 20, 2024 · 1 comment
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enhancement New feature or request

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@Psy-Fer
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Psy-Fer commented Aug 20, 2024

Here is an example of the file format of a seq sum file when bacoding is turned on in minknow

filename_fastq	filename_fast5	filename_pod5	parent_read_id	read_id	run_id	channel	mux	minknow_events	start_time	duration	passes_filtering	template_start	num_events_template	template_duration	sequence_length_template	mean_qscore_template	strand_score_template	median_template	mad_template	pore_type	experiment_id	sample_id	end_reason	alias	type	barcode_arrangement	barcode_full_arrangement	barcode_kit	barcode_variant	barcode_score	barcode_front_id	barcode_front_score	barcode_front_refseq	barcode_front_foundseq	barcode_front_foundseq_length	barcode_front_begin_index	barcode_rear_id	barcode_rear_score	barcode_rear_refseq	barcode_rear_foundseq	barcode_rear_foundseq_length	barcode_rear_end_index
PAW16103_fail_unclassified_438c8a51_ed9a488b_0.fastq.gz	-	PAW16103_438c8a51_ed9a488b_0.pod5	2d43c862-ad44-4609-88b8-86968a0b5c81	2d43c862-ad44-4609-88b8-86968a0b5c81	ed9a488bf2b7687b528a015d5a167792d03de949	246	1	799	16.865600	1.683800	FALSE	16.867600	1401	1.681800	1	1.000000	0.000000	-754.171814	0.007988	not_set	PPTXXS240191	SAMPLE_pool1	signal_positive	unclassified	na	unclassified	LWB01_var1	LWB	var1	-40.000000	BC01_FWD	-40.000000	CCGTGACAAGAAAGTTGTCGGTGTCTTTGTGACTTGCCTGTCGCTCTATCTTC	T	1	0	BC01_REV	-40.000000	GCAATATCAGCACCAACAGAAACACAAAGACACCGACAACTTTCTTGTCACGG	T	1	0
filename_fastq
filename_fast5
filename_pod5
parent_read_id
read_id
run_id
channel
mux
minknow_events
start_time
duration
passes_filtering
template_start
num_events_template
template_duration
sequence_length_template
mean_qscore_template
strand_score_template
median_template
mad_template
pore_type
experiment_id
sample_id
end_reason
alias
type
barcode_arrangement
barcode_full_arrangement
barcode_kit
barcode_variant
barcode_score
barcode_front_id
barcode_front_score
barcode_front_refseq
barcode_front_foundseq
barcode_front_foundseq_length
barcode_front_begin_index
barcode_rear_id
barcode_rear_score
barcode_rear_refseq
barcode_rear_foundseq
barcode_rear_foundseq_length
barcode_rear_end_index
@Psy-Fer Psy-Fer self-assigned this Aug 20, 2024
@Psy-Fer Psy-Fer added the enhancement New feature or request label Aug 20, 2024
@hasindu2008
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I think given we have released this and documented, it is not appropriate to change any column names now. We have to do changes with in these limits
https://github.com/Psy-Fer/buttery-eel/blob/main/docs/formats.md

@Psy-Fer Psy-Fer closed this as completed Sep 7, 2024
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