Ecosyste.ms: Issues

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GitHub / bcgsc/nanosim issues and pull requests

#240 - Metagenomic mode Help with read_analysis.py

Issue - State: open - Opened by florenmartino 27 days ago - 1 comment

#239 - Feature Request: Checking Input-files

Issue - State: open - Opened by SimonHegele 28 days ago - 1 comment
Labels: enhancement

#238 - Add new pre-trained models for metagenome and transcriptome modes

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

#237 - Transcript ID in reference and expression profile do not match

Issue - State: open - Opened by SimonHegele about 2 months ago - 8 comments
Labels: bug

#236 - How many threads and memories required at training stage?

Issue - State: open - Opened by yaoxkkkkk about 2 months ago - 1 comment

#235 - Prepare for release v3.2.2

Pull Request - State: closed - Opened by lcoombe 2 months ago

#234 - Fixes for -min and -max parameters

Pull Request - State: closed - Opened by lcoombe 2 months ago

#233 - Extend lists for simulation in genome mode to avoid IndexError

Pull Request - State: closed - Opened by lcoombe 2 months ago

#232 - Fix for abundance deviation in metagenome mode

Pull Request - State: closed - Opened by lcoombe 2 months ago

#231 - Use more keywords for arguments to alignment functions

Pull Request - State: closed - Opened by lcoombe 3 months ago

#230 - Fixes for transcriptome and metagenome modes

Pull Request - State: closed - Opened by lcoombe 3 months ago

#229 - GPL3 and commercial license

Issue - State: closed - Opened by james-vincent 3 months ago - 2 comments
Labels: question

#226 - `aligner` option missing from `metagenome` characterization mode

Issue - State: closed - Opened by ezherman 3 months ago - 6 comments

#225 - KeyError: "tag 'MD' not present"

Issue - State: open - Opened by mochew 3 months ago - 5 comments

#224 - Prepare for v3.2.1 release

Pull Request - State: closed - Opened by lcoombe 3 months ago

#223 - Fix base quality characterization in chimeric mode

Pull Request - State: closed - Opened by lcoombe 3 months ago

#222 - Fixing characterization stage for genome and metagenome mode with --fastq

Pull Request - State: closed - Opened by lcoombe 3 months ago - 1 comment

#221 - How to simulate amplicon-seq data?

Issue - State: open - Opened by capoony 3 months ago

#220 - Error evaluating base qualities with `read_analysis.py`

Issue - State: closed - Opened by capoony 3 months ago - 3 comments

#219 - Minimap2 version (2.11) co-installed with conda without `--cs` parameter

Issue - State: closed - Opened by capoony 3 months ago - 3 comments

#217 - Homopolymer basequal characterization

Pull Request - State: closed - Opened by SaberHQ 4 months ago

#216 - Simulation of Rolling Circle Amplification Data

Issue - State: closed - Opened by Le1223 4 months ago - 3 comments
Labels: question, wontfix, feature request

#215 - No such file or directory: 'training_ht_length.pkl'

Issue - State: closed - Opened by kubracelikbas 4 months ago - 4 comments

#214 - output different replicates of a sample

Issue - State: closed - Opened by zzare-umd 4 months ago - 1 comment
Labels: question

#213 - Variation in relative abundances of simulated Zymo mock microbes

Issue - State: closed - Opened by ezherman 5 months ago - 7 comments
Labels: help wanted, question

#212 - Effect of `-b` in metagenome mode

Issue - State: closed - Opened by ezherman 5 months ago - 5 comments

#211 - gzip intermediate fastq files

Issue - State: open - Opened by nicolo-tellini 5 months ago
Labels: feature request

#210 - Stuck at the simulation step

Issue - State: open - Opened by HLHsieh 5 months ago - 5 comments
Labels: bug

#209 - Reading the simulated_aligned_reads

Issue - State: closed - Opened by Evandio-Martin 7 months ago - 3 comments

#207 - Questions about the usage and processing of the expression profile

Issue - State: open - Opened by joyceFunk123 8 months ago - 1 comment
Labels: feature request

#206 - Can't install Nanosim

Issue - State: closed - Opened by aerusakovich 8 months ago - 2 comments

#205 - Coverage breadth following metagenome characterization

Issue - State: closed - Opened by ezherman 8 months ago - 2 comments
Labels: question

#204 - How to find reference genome for pre-trained models

Issue - State: closed - Opened by Evandio-Martin 8 months ago - 2 comments
Labels: question

#203 - Installation error

Issue - State: closed - Opened by mfbeuq 10 months ago - 4 comments
Labels: help wanted

#202 - IndexError: list index out of range

Issue - State: open - Opened by weishwu 10 months ago - 4 comments
Labels: bug, question

#201 - Support for Dorado?

Issue - State: closed - Opened by weishwu 10 months ago - 2 comments
Labels: question, feature request

#200 - Options / suggestions for how to simulate nCats data?

Issue - State: open - Opened by tfenne about 1 year ago - 1 comment
Labels: feature request

#199 - Fix infinite loop for very short references

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

#198 - Models for newer versions of Guppy with sup basecalls

Issue - State: open - Opened by hasindu2008 about 1 year ago - 7 comments
Labels: feature request

#197 - Rbk mode

Pull Request - State: open - Opened by GeorgetteTanner over 1 year ago

#196 - Rbk mode

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

#195 - NanoSim for tuning Minimap2 parameters?

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

#194 - simulator.py genome FileNotFoundError: [Errno 2] No such file or directory: 'training_model_profile'

Issue - State: closed - Opened by MAXINELSX over 1 year ago - 2 comments
Labels: question

#193 - Stuck at simulation stage

Issue - State: open - Opened by kainth-amoldeep over 1 year ago - 4 comments
Labels: bug

#192 - Update readme and help info

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

#191 - Please specify the training reads and its reference genome!

Issue - State: closed - Opened by kainth-amoldeep over 1 year ago - 3 comments
Labels: question

#189 - Potential bug-fixes for infinite loops in metagenome mode

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

#188 - Option to specify desired read coverage or sequencing depth

Issue - State: open - Opened by HLHsieh over 1 year ago - 2 comments
Labels: question, feature request

#187 - Models for R10.3 or R10.4 flow cell

Issue - State: closed - Opened by zhenLiuXplr over 1 year ago - 1 comment
Labels: enhancement

#186 - Transcriptome mode error rate tsv explanation

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

#185 - Infinite loop in function extract_reads in metagenome mode when length equals max length

Issue - State: open - Opened by danpal96 almost 2 years ago - 2 comments
Labels: bug, enhancement

#184 - Nanosim hangs in the middle

Issue - State: open - Opened by aastha-batta almost 2 years ago - 18 comments
Labels: bug, help wanted, question

#182 - mis.hist missing when running characterization stage

Issue - State: closed - Opened by lhnguye4 almost 2 years ago

#181 - Invalid fastq format

Issue - State: closed - Opened by xinehc almost 2 years ago - 4 comments
Labels: bug

#180 - Can NanoSim be applied to simulate single cell Nanopore reads

Issue - State: open - Opened by yuntianf almost 2 years ago - 1 comment
Labels: enhancement, feature request

#179 - hangs at start of simulation

Issue - State: closed - Opened by omarkr8 almost 2 years ago - 6 comments
Labels: help wanted, question

#178 - Reads come mostly from one chromosome only

Issue - State: open - Opened by dariober almost 2 years ago - 1 comment
Labels: help wanted, question

#177 - Relax package requirements

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

#176 - Simulating exact number of reads for each input -- transcriptome mode

Issue - State: closed - Opened by kosmasgal about 2 years ago - 2 comments
Labels: help wanted, question, wontfix

#175 - Abnormal error distribution in reads

Issue - State: closed - Opened by zhiliangfu about 2 years ago - 3 comments
Labels: bug

#174 - Could not retrieve index file for alignments

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

#173 - Unexpected phred quality scores with perfect reads

Issue - State: open - Opened by lcoombe about 2 years ago
Labels: bug

#172 - Project dependencies may have API risk issues

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

#171 - Read analysis -- sam_read Parse error.

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

#170 - The meaning of --number in simulator.py

Issue - State: closed - Opened by yanhui09 about 2 years ago - 13 comments

#169 - Update README.md

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

#168 - reads headers empty in fasta file

Issue - State: closed - Opened by jlipovac over 2 years ago - 4 comments
Labels: bug

#167 - fix read headers in metagenome simulation

Pull Request - State: closed - Opened by LokiLuciferase over 2 years ago - 2 comments

#166 - Index out of range errors

Issue - State: open - Opened by RagnarGrootKoerkamp over 2 years ago - 2 comments
Labels: help wanted, question

#165 - No module named `sklearn.neighbours.kde`

Issue - State: closed - Opened by RagnarGrootKoerkamp over 2 years ago - 10 comments
Labels: duplicate, help wanted

#164 - Multithreading bug when using log-normal sampling

Issue - State: open - Opened by 2tony2 over 2 years ago - 3 comments
Labels: help wanted, question

#163 - Output is not reproducible

Issue - State: open - Opened by baraaorabi over 2 years ago - 2 comments
Labels: bug

#162 - NanoSim installation failure

Issue - State: open - Opened by cjwoodruff50 over 2 years ago - 13 comments
Labels: help wanted

#161 - error creating from requirements.txt

Issue - State: closed - Opened by EmersonH2 over 2 years ago - 2 comments

#160 - min_len and max_len options.

Issue - State: open - Opened by XavierGrand over 2 years ago - 2 comments
Labels: bug, feature request

#159 - Update dependent package requirements

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

#158 - Optimize transcriptome simulation

Pull Request - State: closed - Opened by kmnip over 2 years ago - 4 comments

#157 - solve reported issue #155 - fixed read lengths

Pull Request - State: closed - Opened by SaberHQ over 2 years ago

#156 - Reads simulation stuck in an infinite loop or something...

Issue - State: closed - Opened by XavierGrand over 2 years ago - 14 comments
Labels: bug

#155 - Issue of fixed transcriptome read length generated by Nanosim for single thread

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

#153 - typo fix

Pull Request - State: closed - Opened by aafshinfard almost 3 years ago

#152 - Fix error profile read IDs

Pull Request - State: closed - Opened by kmnip almost 3 years ago - 1 comment

#137 - No such file or directory: 'human_strandness_rate'

Issue - State: closed - Opened by mksingh2104 almost 3 years ago - 2 comments

#134 - Are the parameters of the pre-trained models available?

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

#131 - Issue with sklearn.neighbors.kde

Issue - State: closed - Opened by Michal-Babins over 3 years ago - 7 comments

#130 - Could not retrieve index file for primary.bam

Issue - State: closed - Opened by eboileau over 3 years ago - 20 comments

#126 - ValueError: operands could not be broadcast together with shapes

Issue - State: closed - Opened by 865699871 over 3 years ago - 7 comments

#125 - Simulator execution error: "ImportError: No module named request"

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

#120 - Issues with simulator.py and sklearn modules

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

#119 - Sequence length and chimeric positions

Issue - State: closed - Opened by mhuang00 over 3 years ago - 2 comments

#112 - Simulation stops and hangs

Issue - State: open - Opened by molleraj over 3 years ago - 17 comments
Labels: bug, enhancement

#107 - NanoSim produces invalid fastq files

Issue - State: closed - Opened by jkomyno about 4 years ago - 12 comments

#106 - no errors in reads in 1da74ab

Issue - State: closed - Opened by thackl about 4 years ago - 2 comments

#100 - please describe the format of abundance.tsv file

Issue - State: closed - Opened by yhg926 about 4 years ago - 7 comments
Labels: question