Ecosyste.ms: Issues

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GitHub / nanoporetech/duplex-tools issues and pull requests

#55 - merging original duplex bam file with the addtional split duplex bam file

Issue - State: open - Opened by sgujjaBebio about 1 year ago - 1 comment

#54 - numpy<1.24 incompatible with python3.12

Issue - State: closed - Opened by jowodo over 1 year ago - 3 comments

#52 - Low number of good pairs after filtering

Issue - State: open - Opened by myxotheles over 1 year ago - 1 comment

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

Issue - State: open - Opened by dkastl1 over 1 year ago - 5 comments

#50 - split_on_adapter no more than one core?

Issue - State: closed - Opened by KaibondChau over 1 year ago

#49 - np.bool deprecated, package no longer works

Issue - State: closed - Opened by mcrone almost 2 years ago - 1 comment

#48 - couldn't install on linux or pc

Issue - State: closed - Opened by readingradio almost 2 years ago - 5 comments

#47 - issue with split_on_adapter output

Issue - State: open - Opened by itslittman almost 2 years ago - 17 comments

#46 - Unexpected base in duplex call

Issue - State: open - Opened by dpaudel-tb almost 2 years ago - 4 comments

#45 - Extracting duplex reads for multiplexed samples

Issue - State: open - Opened by dpaudel-tb almost 2 years ago - 2 comments

#44 - promethion good pairs: 0

Issue - State: open - Opened by bef22 almost 2 years ago - 3 comments

#43 - question on split pairs

Issue - State: open - Opened by caonetto almost 2 years ago - 3 comments

#42 - pod5 version of duplex_tools issue

Issue - State: closed - Opened by gwl2 almost 2 years ago - 3 comments

#41 - split_pod5 supported seed types error

Issue - State: open - Opened by mp15 almost 2 years ago - 3 comments

#39 - Duplicate reads and read splitting option in MinKNOW

Issue - State: closed - Opened by kaanokay almost 2 years ago - 9 comments

#38 - Update dorado_stereo.sh

Pull Request - State: closed - Opened by mattloose almost 2 years ago - 2 comments

#37 - KeyError: 'sequence_length_template' when basecalling is turned off

Issue - State: closed - Opened by lerminin almost 2 years ago - 2 comments

#36 - empty output from split_pairs

Issue - State: closed - Opened by avilella about 2 years ago - 5 comments

#35 - pairs.txt file empty, but pairs_from_bam/pair_ids.txt not empty

Issue - State: open - Opened by avilella about 2 years ago - 1 comment

#34 - split_pairs not working

Issue - State: closed - Opened by femiliani about 2 years ago - 3 comments

#33 - Update README.md

Pull Request - State: closed - Opened by cfblaeb about 2 years ago - 1 comment

#32 - Cannot install duplex_tools

Issue - State: closed - Opened by BertVanm about 2 years ago - 2 comments

#31 - problem with Fastx

Issue - State: closed - Opened by sheucke about 2 years ago - 2 comments

#30 - Unexpected input file name changes output file file name format on split_on_adapter

Issue - State: open - Opened by groodri about 2 years ago - 1 comment
Labels: bug

#29 - Question - Split on adapter

Issue - State: open - Opened by jagos01 about 2 years ago - 10 comments

#28 - Try edlib for faster duplex matching

Issue - State: open - Opened by olawa about 2 years ago - 1 comment

#27 - filter_pairs fails if both fastq and aligned bam are present

Issue - State: closed - Opened by olawa about 2 years ago - 3 comments

#26 - config/base calling models

Issue - State: closed - Opened by CharlotteAnne over 2 years ago - 2 comments
Labels: question

#25 - Combining reads post duplex basecalling for assembly

Issue - State: open - Opened by surabhiranavat over 2 years ago - 5 comments

#24 - base quality scores

Issue - State: closed - Opened by osilander over 2 years ago - 4 comments
Labels: question

#23 - Feature request: specify number of threads

Issue - State: closed - Opened by osilander over 2 years ago - 2 comments

#22 - Not all sub reads from multiple splits are written to FASTQ output file

Issue - State: closed - Opened by callumparr over 2 years ago - 4 comments

#21 - Split_on_adapter and sample type

Issue - State: closed - Opened by Thomieh73 over 2 years ago - 5 comments

#20 - False positives in filter_pairs when run on linearized plasmid

Issue - State: closed - Opened by eyesmo over 2 years ago - 4 comments

#19 - specify custom adapters to split_on_adapter

Issue - State: open - Opened by MortenEneberg over 2 years ago - 14 comments

#18 - Document the relationship between ont-guppy-duplex-pipeline and duplex_tools

Issue - State: open - Opened by tbooth over 2 years ago - 3 comments

#17 - Combining split_on_adapter with duplex calling

Issue - State: open - Opened by Coryza over 2 years ago - 7 comments

#16 - Several uncertainties

Issue - State: closed - Opened by claumer over 2 years ago - 1 comment

#15 - Fix setup metadata repo URL.

Pull Request - State: closed - Opened by cbrueffer over 2 years ago - 1 comment
Labels: enhancement

#13 - allow multiple splits does not work with test duplication

Issue - State: closed - Opened by callumparr over 2 years ago - 12 comments

#12 - Can this split read into more than 2 subreads?

Issue - State: closed - Opened by callumparr over 2 years ago - 10 comments

#11 - Specify model?

Issue - State: closed - Opened by adbeggs over 2 years ago - 1 comment

#10 - guppy_basecaller_duplex generated six fastq files from 252 fast5 files....

Issue - State: closed - Opened by MostafaYA almost 3 years ago - 1 comment

#9 - slow pairing process

Issue - State: closed - Opened by olawa almost 3 years ago - 21 comments

#8 - how to use assess_split_on_adapter

Issue - State: closed - Opened by defendant602 about 3 years ago - 1 comment

#7 - TypeError: mkdir() got an unexpected keyword argument 'exist_ok'

Issue - State: closed - Opened by defendant602 about 3 years ago - 5 comments

#6 - Only works with gzipped fastq files

Issue - State: closed - Opened by mitenjain over 3 years ago - 4 comments

#5 - duplex_tools filter_pairs failed on *fastq.gz files produced by Promethion

Issue - State: closed - Opened by ChuShin over 3 years ago - 6 comments

#4 - duplex_tools filter_pairs to have min and max length options?

Issue - State: closed - Opened by Kirk3gaard over 3 years ago - 2 comments

#3 - Which release of guppy has guppy_basecaller_duplex?

Issue - State: closed - Opened by Kirk3gaard over 3 years ago - 1 comment

#2 - Error in running split_on_adapter

Issue - State: closed - Opened by Serka-M over 3 years ago - 3 comments

#1 - Unclear usage

Issue - State: closed - Opened by markme123 over 3 years ago - 1 comment