Ecosyste.ms: Issues

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GitHub / davidsongroup/flexiplex issues and pull requests

#51 - Update documentation for flexiplex-filter

Issue - State: closed - Opened by nadiadavidson 2 months ago - 3 comments

#50 - Add citation info to usage and end of run

Issue - State: closed - Opened by nadiadavidson 3 months ago - 1 comment
Labels: enhancement

#49 - Add ATAC barcode to defaults

Issue - State: open - Opened by nadiadavidson 3 months ago
Labels: enhancement

#48 - Best practice for pipelines

Issue - State: open - Opened by ljwharbers 3 months ago - 4 comments

#47 - overwrite old stats file instead of appending

Pull Request - State: open - Opened by ChangqingW 4 months ago

#46 - add CB UB tag to fastq id field

Pull Request - State: closed - Opened by ChangqingW 5 months ago

#45 - Degenerate bases

Issue - State: closed - Opened by cnk113 8 months ago - 1 comment

#44 - barcode and umi opposite sides and whitelist optimizations

Issue - State: closed - Opened by ljwharbers 8 months ago - 6 comments

#43 - Panic due to out of range error when finding the substring

Issue - State: closed - Opened by olliecheng 10 months ago - 9 comments

#42 - out_of_range error in substr

Pull Request - State: closed - Opened by ChangqingW 10 months ago - 1 comment

#41 - reads with two barcode and one umi

Issue - State: closed - Opened by ashokpatowary 10 months ago - 12 comments

#40 - Processing time

Issue - State: closed - Opened by nrhorner 10 months ago - 3 comments

#39 - Fix Github Action build on HPC (libc 2.17)

Pull Request - State: closed - Opened by olliecheng 11 months ago

#38 - Action to automatically build on x64 Linux and arm64/x64 macOS

Pull Request - State: closed - Opened by olliecheng 11 months ago

#37 - Flexiplex barcode count clarification?

Issue - State: closed - Opened by cnk113 11 months ago - 1 comment

#36 - Add a flag to report chimeric reads

Pull Request - State: closed - Opened by olliecheng 11 months ago

#35 - Try trim remainder of the polyT

Pull Request - State: open - Opened by ChangqingW 11 months ago

#34 - Dual barcodes

Issue - State: closed - Opened by gwaldbieser 11 months ago - 1 comment

#33 - Fix flexiplex_filter bug caused by small barcode lists

Pull Request - State: closed - Opened by olliecheng 11 months ago

#32 - Enable barcode and UMI length to be given, instead of a sequence of ?'s

Issue - State: open - Opened by olliecheng about 1 year ago
Labels: low-priority

#31 - adding verbose flag

Issue - State: closed - Opened by ghar1821 about 1 year ago - 7 comments
Labels: low-priority

#30 - Fix issue where left search index is out of bounds

Pull Request - State: closed - Opened by olliecheng about 1 year ago

#29 - std::out_of_range when mapping reads

Issue - State: closed - Opened by ghar1821 about 1 year ago - 4 comments

#27 - rename file to reads_ifs

Pull Request - State: closed - Opened by ChangqingW over 1 year ago - 5 comments

#26 - Segfault when running with process substitution on MacOS

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

#25 - Add conda test for demultipex outputs; trim polyT

Pull Request - State: closed - Opened by ChangqingW over 1 year ago - 5 comments

#24 - Upper limit for flexiplex_filter

Issue - State: closed - Opened by nadiadavidson over 1 year ago - 2 comments

#23 - More customisable barcode patterns

Pull Request - State: closed - Opened by ChangqingW over 1 year ago - 5 comments

#22 - Build & packaging changes

Pull Request - State: closed - Opened by olliecheng over 1 year ago

#21 - Limiting search space or reporting distance from 5' / 3' ends

Issue - State: closed - Opened by yxsee over 1 year ago - 1 comment

#20 - UMI before barcode

Issue - State: closed - Opened by yxsee over 1 year ago - 2 comments

#19 - Sequences used for 5' ONT

Issue - State: closed - Opened by mcortes-lopez over 1 year ago - 5 comments

#18 - Add rank data after whitelist filtration

Pull Request - State: closed - Opened by olliecheng over 1 year ago

#17 - Add filter-barcodes.py to documentation

Pull Request - State: closed - Opened by olliecheng over 1 year ago

#15 - Exclude ambiguous barcodes etc.

Pull Request - State: closed - Opened by ChangqingW over 1 year ago - 7 comments

#13 - Change endls to \n

Pull Request - State: closed - Opened by edoyango over 1 year ago - 1 comment

#12 - Automatically estimate number of cells for discovery mode.

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

#9 - Adding option to report UMI barcode in _reads_barcodes.txt output file?

Issue - State: closed - Opened by shuyi-w almost 2 years ago - 1 comment
Labels: wontfix

#8 - Possibility of UMI deduplication from flexiplex output

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

#7 - Forward and reverse barcode

Issue - State: closed - Opened by Frazapel about 2 years ago - 1 comment

#6 - flexiplex: command not found

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

#5 - Add option to report reads with no match

Issue - State: open - Opened by nadiadavidson about 2 years ago
Labels: enhancement

#4 - Support for bams?

Issue - State: open - Opened by nadiadavidson about 2 years ago - 1 comment
Labels: enhancement

#3 - Explicit NA for empty columns in output file

Issue - State: closed - Opened by ghar1821 over 2 years ago

#2 - Duplication of reads with barcodes on +/- strand

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

#1 - Multi-thread option

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