Ecosyste.ms: Issues

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GitHub / malonge/RagTag issues and pull requests

#193 - error during scaffolding..unable to get scaffold.fasta

Issue - State: closed - Opened by karthickbrlab about 1 month ago

#192 - The possibility of starting from HiFi ccs reads

Issue - State: open - Opened by OceanLyu 4 months ago

#191 - integration with juicer

Issue - State: open - Opened by Overcraft90 4 months ago

#190 - Scaffold option -r error

Issue - State: closed - Opened by arif-tanmoy 5 months ago

#189 - question of Hi-C to resolve conflicts

Issue - State: open - Opened by njliangdong 5 months ago

#187 - RagTag error: "OSError: error when opening file"

Issue - State: open - Opened by ylzou867 6 months ago - 1 comment

#185 - ragtag.patch.fasta lacks unplaced contigs?

Issue - State: closed - Opened by adadiehl 7 months ago - 1 comment

#184 - Missing ragtag.correct.reads.s.bam file

Issue - State: open - Opened by faye-romero 7 months ago - 1 comment

#183 - Scaffold and correct

Issue - State: open - Opened by aabaricalla 8 months ago - 1 comment

#181 - output file not found

Issue - State: open - Opened by Anysdn 8 months ago

#178 - Speed RagTag up a few orders of magnitude on fragmented assemblies with caching

Pull Request - State: open - Opened by twrightsman about 1 year ago - 1 comment

#177 - Ragtag Merge IndexError for -f AGP file

Issue - State: open - Opened by nickgladman about 1 year ago

#176 - ERROR: encountered an invalid zero or negative numeric AGP field.

Issue - State: closed - Opened by wshuai294 about 1 year ago - 1 comment

#175 - patch output genome is identical to input target genome

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

#174 - Error when running RagTag patch command

Issue - State: closed - Opened by nvuhunganh about 1 year ago - 1 comment

#173 - pysam error

Issue - State: open - Opened by mabh5 about 1 year ago

#172 - Scaffold longer than reference genome due to NNNNs

Issue - State: open - Opened by vappiah about 1 year ago - 3 comments

#171 - Can't use multiple threads via -t

Issue - State: open - Opened by ChungLamYu over 1 year ago - 3 comments

#168 - `ragtag scaffold` without concatenation

Issue - State: open - Opened by taprs over 1 year ago

#166 - updategff issues

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

#164 - Unable to fill gap with ragtag scaffold and patch

Issue - State: open - Opened by yipukangda over 1 year ago

#163 - correct use by the species.

Issue - State: open - Opened by danielpinilla1 over 1 year ago - 1 comment

#162 - RagTAg correct: "no attribute 'get_reference_length'"

Issue - State: closed - Opened by pna059 over 1 year ago - 1 comment

#161 - Running RagTag on bacterial short-read assemblies

Issue - State: open - Opened by ne1al almost 2 years ago

#160 - Large >270Mb contigs vs >14Gb reference

Issue - State: open - Opened by Ural-Yunusbaev almost 2 years ago

#159 - Question about installation

Issue - State: open - Opened by zhousun21 almost 2 years ago - 1 comment

#158 - A question about "correct" step in RagTag, I need help!

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

#157 - Scaffold inserting strings of 100 N's?

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

#155 - RagTag patch bug

Issue - State: open - Opened by r-poloni almost 2 years ago - 4 comments

#154 - Scaffold doesn't run

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

#153 - Cases where missassembly correction and patching aren't needed

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

#152 - Patch error: "Tuple Index out of Range"

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

#151 - How to pass minimap2 parameters?

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

#150 - repeat masking

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

#149 - RagTag name coming up

Issue - State: open - Opened by rmormando about 2 years ago

#148 - Some contigs are not scaffolded

Issue - State: open - Opened by rknx about 2 years ago

#147 - RagTag Reference

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

#146 - Error message when running ragtag_scaffold.py

Issue - State: open - Opened by Surbhigrewal about 2 years ago

#144 - about paf2delta

Issue - State: open - Opened by 1085268616 about 2 years ago - 1 comment

#142 - Split assembly at BED coordinates

Pull Request - State: open - Opened by Neato-Nick about 2 years ago - 1 comment

#141 - a bytes-like object is required, not 'dict'

Issue - State: open - Opened by mabh5 about 2 years ago - 8 comments

#140 - the reference file was

Issue - State: open - Opened by H1207953831 over 2 years ago

#139 - Error in patch command

Issue - State: open - Opened by akhtarmzn2010 over 2 years ago - 1 comment

#138 - ragtag patch didn't work as expected in haplotype assembly

Issue - State: open - Opened by HippoYI over 2 years ago

#137 - -t option not working during the correct step

Issue - State: open - Opened by tamascogustavo over 2 years ago

#135 - Enhanced GFF updating

Pull Request - State: open - Opened by Neato-Nick over 2 years ago

#134 - Inconsistent input files for update_gff

Issue - State: open - Opened by Neato-Nick over 2 years ago - 2 comments

#133 - update vcf file from pre-scaffold genome to ragtag genome

Issue - State: open - Opened by 38293649 over 2 years ago

#132 - RagTag.py merge

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

#130 - Runtimeerr, patch

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

#129 - a bug for the last step of merge

Issue - State: open - Opened by CrawlingSponge over 2 years ago - 1 comment

#128 - Which utility to use to stitch scaffolds into a single assembly

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

#127 - Error for path step

Issue - State: open - Opened by dtx282000 over 2 years ago

#126 - glibc UnsatisfiableError:

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

#125 - Sequence of GAPs filled by ragtag patch

Issue - State: open - Opened by mirkocelii over 2 years ago

#124 - AGP2FA: KeyError: "sequence 'tig00001068' not present"

Issue - State: closed - Opened by leone93 over 2 years ago - 2 comments

#121 - Troubling in patching?

Issue - State: open - Opened by jun3234 over 2 years ago

#120 - problems with scaffolded contig ids

Issue - State: open - Opened by eddykay310 over 2 years ago - 2 comments

#119 - How does patch handle sequence names?

Issue - State: open - Opened by FGoettelmann over 2 years ago - 1 comment

#118 - the length of scaffolds generated by ragtag is not

Issue - State: open - Opened by ardy20 over 2 years ago

#117 - The bug when run the ragtag.py merge command

Issue - State: open - Opened by Jiangjiangzhang6 almost 3 years ago

#116 - How to determine the number of ref.fasta.

Issue - State: open - Opened by abcyulongwang almost 3 years ago - 1 comment

#115 - How to provide paired end short reads to RagTag correct?

Issue - State: open - Opened by ceanothus almost 3 years ago - 1 comment

#114 - Adding wfmash as alinger

Issue - State: open - Opened by baozg almost 3 years ago - 2 comments
Labels: enhancement

#113 - scaffolding issues

Issue - State: open - Opened by eddykay310 almost 3 years ago

#112 - Old gff file transform to new gff file

Issue - State: closed - Opened by wq-ls almost 3 years ago

#111 - ValueError: Input AGPs do not have the same set of components.

Issue - State: closed - Opened by linshengnan09 almost 3 years ago - 3 comments

#110 - Patch seqs input (Hifi contigs to fill ONT ultra-long assembly gaps)?

Issue - State: closed - Opened by hrluo93 almost 3 years ago - 1 comment

#109 - Scaffolding Error

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

#108 - Query sequence in patch function

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

#107 - Asking RagTag correction and scaffold running time

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

#106 - Scaffolding non-model plant genomes

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

#105 - scaffolding with inverted genomic region

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

#104 - RagTag and regions of heterozygosity

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

#103 - Error in merge with Hi-C related to bam index

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

#101 - Question Ragtag scaffold command parameters

Issue - State: open - Opened by Saveli01 about 3 years ago - 4 comments
Labels: enhancement

#100 - Question about unexpected gaps

Issue - State: closed - Opened by zhousun21 about 3 years ago - 2 comments

#99 - Error in merge with Hi-C data

Issue - State: open - Opened by Shokusei about 3 years ago - 2 comments
Labels: bug

#98 - Hi-C to correct

Issue - State: closed - Opened by Johnsonzcode about 3 years ago - 9 comments

#96 - How to understand patch

Issue - State: closed - Opened by Yutang-ETH about 3 years ago - 4 comments

#95 - RagTag "patch" not outputting all the results

Issue - State: closed - Opened by DuttaAnik about 3 years ago - 7 comments

#94 - ERROR: object identifier out of order

Issue - State: open - Opened by zanfona734 about 3 years ago - 15 comments
Labels: bug

#93 - Why not use Nucmer 4?

Issue - State: closed - Opened by Yutang-ETH about 3 years ago - 8 comments