duplex-tools

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merging original duplex bam file with the addtional split duplex bam file

1

Hi, I would like to clarify if you would recommend merging the final duplex bam files: duplex_orig.sam duplex_splitduplex.sam Thanks

sgujjaBebio

Hi, I am trying to use the "split_on_adapter" functionality to split chimeric ONT reads into sub-reads. Since we are using different adapters and primers than the one specified in the...

Gazal90

Low number of good pairs after filtering

1

Hi, I am trying to get duplex sequencing up but I find I get a very low number of 'good pairs' after filtering and consenquently, a very low number of...

myxotheles

guppy_duplex ValueError: not enough values to unpack (expected 4, got 3)

5

When I try to run guppy_duplex on my fast5 files, it successfully completes simplex basecalling but then gives the error `ValueError: not enough values to unpack (expected 4, got 3)`...

dkastl1

issue with split_on_adapter output

17

I successfully ran split_on_adapter with the --allow-multiple-splits option and it split a bunch of reads for me. When converting the new mapped SAM file to BAM format, it wrote about...

itslittman

split_pod5 supported seed types error

3

When running: ``` $ duplex_tools --version Duplex Sequencing Tools 0.3.2 $ python --version Python 3.11.0 $ duplex_tools split_pairs --threads 2 dorado.moves.bam OESO_152_LSK114/20230322_1606_3G_PAO27011_7b4991d0/ OESO_152_LSK114_pod5s_splitduplex/ ``` I get the following exception: ```...

mp15

Unexpected base in duplex call

4

Hello, I extracted fastq from the duplex_orig.sam and compared output to the original raw reads. In the following alignment file, The top sequence is the output for the duplex read....

dpaudel-tb

Extracting duplex reads for multiplexed samples

2

Since barcoding is still under development in darado, I was wondering what alternative approach would be a proper way to extract duplex reads for multiplexed samples? I am thinking along...

dpaudel-tb

promethion good pairs: 0

3

Hi I'm using duplex_tools filter_pairs (duplex tools version: 0.3.2) on promethion created fastq files and out of 2759916 duplex pairs none are reported good. I did find the issue where...

bef22

question on split pairs

3

When running split pairs on pod5s and the basecalled sam, duplex tools generates a new folder with split pod5 files and associated read ids. Does this folder contain all the...

caonetto