Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bcgsc/arcs issues and pull requests

#170 - Fix ubuntu CI

Pull Request - State: closed - Opened by lcoombe about 1 month ago

#169 - downloading conda in macOS CI tests

Pull Request - State: closed - Opened by emilyyzhangg about 2 months ago

#100 - formatting fastq data correctly

Issue - State: closed - Opened by bioinfowheat almost 4 years ago - 3 comments
Labels: question

#99 - ARCS finds 0 barcodes when using TELLSeq reads instead of Chromium reads

Issue - State: closed - Opened by grendon almost 4 years ago - 3 comments

#98 - arcs-long functionality

Pull Request - State: closed - Opened by theottlo about 4 years ago

#97 - Add stale.yml

Pull Request - State: closed - Opened by lcoombe about 4 years ago

#96 - Boost 1.58.0 address

Issue - State: closed - Opened by REDitter over 4 years ago - 1 comment
Labels: bug

#95 - Number of Ns

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

#94 - Sideloading a BAM

Issue - State: closed - Opened by andreaswallberg over 4 years ago - 4 comments
Labels: question, stale

#93 - Error ARCS: sequence with ID "X" empty

Issue - State: closed - Opened by mas160 over 4 years ago - 7 comments
Labels: stale

#92 - Alignment using longranger and variant calling best practices

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

#91 - mapping with BWA versus LONGRANGER ALIGN

Issue - State: closed - Opened by burri-wildlight over 4 years ago - 4 comments
Labels: question

#90 - question about the long ranger basic

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

#89 - arcs dies with error: `@HD VN:1.3 SO:coordinate': No such file or directory

Issue - State: closed - Opened by claumer almost 5 years ago - 5 comments
Labels: question

#88 - Arcs.cpp: fix binomial bug

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 8 comments

#87 - no such file or directory: /tigmint-molecule

Issue - State: closed - Opened by mas160 almost 5 years ago - 14 comments
Labels: question

#86 - checkSignificance when second == 0?

Issue - State: closed - Opened by lcoombe almost 5 years ago - 6 comments

#85 - arcs-tigmint error

Issue - State: closed - Opened by mas160 almost 5 years ago - 1 comment

#84 - arcs-make tigmint command not found

Issue - State: closed - Opened by mas160 almost 5 years ago - 7 comments
Labels: question

#83 - output pairing information

Pull Request - State: closed - Opened by jwcodee almost 5 years ago

#82 - Clang format

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: enhancement

#81 - Set up CI with Azure Pipelines

Pull Request - State: closed - Opened by lcoombe almost 5 years ago

#80 - output pairing information

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 1 comment
Labels: invalid

#79 - question about 'Barcode whitelist filtering'

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

#78 - About contig length & Scaffold length

Issue - State: closed - Opened by EugeneKim76 about 5 years ago - 2 comments
Labels: question

#77 - Error 11 when running arks + links pipeline

Issue - State: closed - Opened by Pikayy about 5 years ago - 9 comments
Labels: question

#76 - question about the parameters -m and -d

Issue - State: closed - Opened by longzhangnation about 5 years ago - 5 comments
Labels: question

#75 - Too much data?

Issue - State: closed - Opened by sunnycqcn about 5 years ago - 4 comments

#74 - LICENSE file missing

Issue - State: closed - Opened by bgruening about 5 years ago - 1 comment

#73 - Install arcs with error about gcc

Issue - State: closed - Opened by sunnycqcn about 5 years ago - 7 comments

#72 - It is the same readme file!

Issue - State: closed - Opened by sunnycqcn about 5 years ago - 4 comments
Labels: question

#71 - Mapping using longranger

Issue - State: closed - Opened by RNieuwenhuis about 5 years ago - 3 comments
Labels: question

#70 - update readMe and arcs-make

Pull Request - State: closed - Opened by MurathanGoktas about 5 years ago - 1 comment

#69 - Update read me arks

Pull Request - State: closed - Opened by MurathanGoktas about 5 years ago - 3 comments

#68 - Polyploid analysis

Issue - State: closed - Opened by trgibbons over 5 years ago - 1 comment

#67 - Merge ARKS into ARCS

Pull Request - State: closed - Opened by MurathanGoktas over 5 years ago

#66 - Problems with arcs-make

Issue - State: closed - Opened by majogomezhughes over 5 years ago - 13 comments
Labels: question

#65 - Barcode multiplicity fix

Pull Request - State: closed - Opened by MurathanGoktas over 5 years ago - 6 comments

#64 - arcs-make command format question

Issue - State: closed - Opened by pal263 over 5 years ago - 1 comment
Labels: question

#63 - unable to correctly compile with make

Issue - State: closed - Opened by Sparkle-27 over 5 years ago - 6 comments
Labels: question

#62 - Can't get the correct fastq format from longranger

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

#61 - Error in running demo of ARCS

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

#60 - How can I decrease missing data in my draft genome

Issue - State: closed - Opened by scintilla9 over 5 years ago - 5 comments

#59 - unpaired reads issue

Issue - State: closed - Opened by dcopetti over 5 years ago - 3 comments
Labels: question

#58 - issue with Autotools

Issue - State: closed - Opened by dcopetti over 5 years ago - 2 comments
Labels: question

#57 - Supernova fasta output

Issue - State: closed - Opened by pstokespmb over 5 years ago - 2 comments
Labels: question

#56 - Recommendation on multiple lanes

Issue - State: closed - Opened by erondeau over 5 years ago - 1 comment

#55 - unusual behavior of tigmint

Issue - State: closed - Opened by plw1080 almost 6 years ago - 3 comments

#54 - number of scaffolds == number of contigs

Issue - State: closed - Opened by chen42 almost 6 years ago - 7 comments

#53 - arcs-make pipeline query

Issue - State: closed - Opened by plw1080 almost 6 years ago - 2 comments
Labels: question

#52 - [E::bgzf_flush] File write failed (wrong size)

Issue - State: closed - Opened by stevehilo almost 6 years ago - 3 comments
Labels: question

#51 - arcs-make location

Issue - State: closed - Opened by plw1080 almost 6 years ago - 3 comments

#50 - Problem with ARCS with or without Tigmint

Issue - State: closed - Opened by agroppi almost 6 years ago - 3 comments
Labels: question

#49 - N50 decreased from Supernova to Tigmint-ARCS-LINKS

Issue - State: closed - Opened by Dharmendra-G-1 almost 6 years ago - 2 comments
Labels: question

#48 - problem with tigmint-cut

Issue - State: closed - Opened by Dharmendra-G-1 almost 6 years ago - 5 comments

#47 - Tuning -e parameter

Issue - State: closed - Opened by harish0201 almost 6 years ago - 3 comments
Labels: question

#46 - Absolut zero scaffolding

Issue - State: closed - Opened by francicco almost 6 years ago - 11 comments

#45 - AGP file creation

Issue - State: closed - Opened by shameem356 almost 6 years ago - 1 comment

#44 - Correct fastq format

Issue - State: closed - Opened by francicco almost 6 years ago - 9 comments

#43 - what is the mean about c and a parameters?

Issue - State: closed - Opened by sunnycqcn about 6 years ago - 3 comments

#42 - I get nothing in original.gv file

Issue - State: closed - Opened by JhinAir about 6 years ago - 2 comments

#41 - Running problem

Issue - State: closed - Opened by JhinAir about 6 years ago - 3 comments

#40 - BAM FILES input

Issue - State: closed - Opened by Grelot about 6 years ago - 2 comments
Labels: question

#39 - New dist estimate

Pull Request - State: closed - Opened by jtse02 about 6 years ago - 1 comment
Labels: enhancement, stale

#38 - miBF support

Pull Request - State: closed - Opened by jtse02 about 6 years ago - 1 comment
Labels: stale

#37 - small correction for parallelisation of bwa in arcs-make

Issue - State: closed - Opened by rahulvrane over 6 years ago - 1 comment

#36 - empty _original.gv file

Issue - State: closed - Opened by mossishahi over 6 years ago - 35 comments

#35 - error: `@HD VN:1.5 SO:unknown': No such file or directory

Issue - State: closed - Opened by shtist over 6 years ago - 2 comments

#34 - inconsistent use of spaces and tabs in makeTSVfile.py

Issue - State: closed - Opened by jdmontenegro over 6 years ago - 1 comment

#33 - error in bam file?

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

#32 - Length of fasta sequences vs @SQ and masking

Issue - State: closed - Opened by mp15 over 6 years ago - 6 comments
Labels: bug

#30 - Use the BX:Z tag if present, and read sequence lengths from SAM header

Pull Request - State: closed - Opened by sjackman over 6 years ago - 6 comments

#29 - Set default end length to 30k.

Pull Request - State: closed - Opened by jvhaarst almost 7 years ago - 2 comments

#28 - End length is not 30k by default.

Issue - State: closed - Opened by jvhaarst almost 7 years ago - 3 comments

#27 - readBAM: The last underscore separates the barcode

Pull Request - State: closed - Opened by sjackman almost 7 years ago - 2 comments
Labels: bug

#26 - chimeric scaffolds detection with ARCS

Issue - State: closed - Opened by dcopetti almost 7 years ago - 2 comments
Labels: question

#25 - compile error: using ‘typename’ outside of template

Issue - State: closed - Opened by billzt almost 7 years ago - 2 comments

#24 - empty XXXX_original.gv file

Issue - State: closed - Opened by tiramisutes almost 7 years ago - 3 comments

#23 - samtools: Not a directory

Issue - State: closed - Opened by tiramisutes almost 7 years ago

#22 - running ARCS multiple times using newly scaffolded assembly as a reference

Issue - State: closed - Opened by mikoze about 7 years ago - 6 comments

#21 - How may mis-scaffolding happen

Issue - State: closed - Opened by qihualiang about 7 years ago - 6 comments

#20 - Configure problem with write_graphviz_dp

Issue - State: closed - Opened by ValentinaPeona over 7 years ago - 5 comments

#19 - Mean gaps in .scaffolds csv file are all the same

Issue - State: closed - Opened by Hazelhuangup over 7 years ago - 11 comments

#18 - N50 become smaller while increasing the reads depth

Issue - State: closed - Opened by conniecl over 7 years ago - 2 comments

#17 - Link to paper and LINKS software in README.md ?

Issue - State: closed - Opened by jvhaarst over 7 years ago - 1 comment

#16 - Make linecount larger, and fix some typos.

Pull Request - State: closed - Opened by jvhaarst over 7 years ago

#15 - empty graph.gv file

Issue - State: closed - Opened by Hazelhuangup over 7 years ago - 2 comments

#14 - Too large BAM file ?

Issue - State: closed - Opened by jvhaarst over 7 years ago - 6 comments

#13 - Remove hard coded barcode length, and some cleanup

Pull Request - State: closed - Opened by jvhaarst over 7 years ago - 1 comment
Labels: stale

#12 - Configure complains about unary operator

Issue - State: closed - Opened by jvhaarst over 7 years ago - 8 comments
Labels: bug

#11 - Could not open @HD VN:1.3 SO:coordinate. --fatal

Issue - State: closed - Opened by shameem356 over 7 years ago - 6 comments

#10 - The Influence of PCR duplicates on Arcs

Issue - State: closed - Opened by danshu almost 8 years ago - 3 comments

#9 - Empty graph when running ARCS

Issue - State: closed - Opened by fg6 almost 8 years ago - 36 comments

#8 - Barcode length for Arcs

Issue - State: closed - Opened by danshu almost 8 years ago - 2 comments

#7 - Pick up chromium barcode from BX tag

Issue - State: closed - Opened by johandahlberg almost 8 years ago - 7 comments
Labels: enhancement

#6 - How is LINKS using .gv and .tsv files?

Issue - State: closed - Opened by peterdfields almost 8 years ago - 6 comments

#5 - Problem running makeTSVfile.py

Issue - State: closed - Opened by stephenrdoyle almost 8 years ago - 9 comments

#4 - Instruction on tuning parameters?

Issue - State: closed - Opened by danshu almost 8 years ago - 4 comments
Labels: question

#3 - Error in sorting order of BAM files

Issue - State: closed - Opened by danshu almost 8 years ago - 4 comments