Ecosyste.ms: Issues

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GitHub / MrOlm/inStrain issues and pull requests

#107 - Tutorial 1 comparison error

Issue - State: closed - Opened by iwilkie over 2 years ago - 14 comments

#106 - Issue of "I dont know how to process ... (the gene file)"

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

#105 - Can Instrain differentiate between read_ids for paired-end file in bam file?

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

#104 - InStrain for PacBio longreads

Issue - State: open - Opened by DanielSpari over 2 years ago - 3 comments
Labels: enhancement

#103 - The question for running command "inStrain profile"

Issue - State: closed - Opened by toggle0511 almost 3 years ago - 4 comments

#102 - null model seems not being consistently applied leading to wrong allelle_counts

Issue - State: closed - Opened by zhaoc1 almost 3 years ago - 5 comments

#101 - multiprocessing error

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

#100 - Minimum files for compare

Issue - State: closed - Opened by kirkgrubbs1 about 3 years ago - 3 comments

#99 - Coverage discrepancy with inStrain profile

Issue - State: open - Opened by cswift3 about 3 years ago - 6 comments
Labels: enhancement

#98 - Distributing Comparisons

Issue - State: closed - Opened by kirkgrubbs1 about 3 years ago - 11 comments
Labels: enhancement

#97 - inStrain compare gives "You're comparing ISP profiles that have the same names." message

Issue - State: closed - Opened by jdwinkler-lanzatech about 3 years ago - 3 comments
Labels: enhancement

#96 - allele frequency

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

#95 - inStrain compare not printing strain_clusters.tsv

Issue - State: closed - Opened by clb21565 about 3 years ago - 4 comments

#94 - Pass input profiles in text file to inStrain compare

Issue - State: open - Opened by jdwinkler-lanzatech about 3 years ago - 2 comments
Labels: enhancement

#92 - Insights regarding nucleotide diversity vs SNVs

Issue - State: closed - Opened by DDavila10 over 3 years ago - 5 comments

#91 - Read trimming

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

#90 - Subsetting reads / minimum MAG quality thresholds

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

#88 - Issue with running basic inStrain command.

Issue - State: closed - Opened by ivanjm422 over 3 years ago - 2 comments

#87 - Detecting indels

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

#86 - Step resource optimization and filter_reads

Issue - State: closed - Opened by kirkgrubbs1 over 3 years ago - 3 comments

#85 - Insights regarding nucleotide diversity

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

#84 - Outputting genome consensus sequences

Issue - State: closed - Opened by jasonarothman over 3 years ago - 2 comments
Labels: enhancement

#83 - Using non-prodigal gene calls

Issue - State: open - Opened by jdwinkler-lanzatech over 3 years ago - 11 comments
Labels: enhancement

#82 - Error due to duplicated contig names in custom MAG db

Issue - State: closed - Opened by franciscozorrilla over 3 years ago - 10 comments

#81 - Small typo fixes in docs page important_concepts

Pull Request - State: closed - Opened by franciscozorrilla over 3 years ago - 1 comment

#80 - Problem to running inStrain profile

Issue - State: closed - Opened by DDavila10 over 3 years ago - 2 comments

#79 - inStrain compare assertion error: You're comparing ISP profiles that have the same names.

Issue - State: closed - Opened by zhaoc1 over 3 years ago - 4 comments
Labels: documentation

#78 - dRep 99% vs InStrain for pangenome analysis

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

#77 - Getting high number of SNS in reads that I used for Generation of SRGs

Issue - State: closed - Opened by DDavila10 over 3 years ago - 4 comments

#76 - Fails after filtering reads: no paired reads

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

#75 - Compare stalls when using multiple processes:

Issue - State: closed - Opened by EisenRa over 3 years ago - 1 comment
Labels: system specific bug

#74 - inStrain compare result questions

Issue - State: closed - Opened by jmartin77777 over 3 years ago - 1 comment

#73 - Question about metagenomic SNP-calling

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

#72 - Issue with Single End Reads

Issue - State: closed - Opened by rusher321 over 3 years ago - 1 comment

#71 - Question about inStrain compare dendrograms

Issue - State: closed - Opened by jmartin77777 over 3 years ago - 4 comments
Labels: documentation

#70 - more filtered reads than raw reads?

Issue - State: closed - Opened by rebeccasophiasalcedo over 3 years ago - 7 comments
Labels: documentation

#69 - genome coverage

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

#68 - `instrain profile`: 15 hours and counting

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

#67 - error message = 'No locks available'

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

#66 - Script exiting at start of Step 2. Profile scaffolds

Issue - State: closed - Opened by jmartin77777 almost 4 years ago - 7 comments

#65 - Update tutorial.rst

Pull Request - State: closed - Opened by rusher321 almost 4 years ago - 1 comment

#64 - log file output

Issue - State: closed - Opened by ramiroricardo almost 4 years ago - 1 comment

#63 - Issue with Paired End Reads from SRA

Issue - State: closed - Opened by elizabethmcd almost 4 years ago - 2 comments

#62 - Get Raw Data from readANI_distribution plot

Issue - State: open - Opened by elizabethmcd almost 4 years ago - 2 comments
Labels: enhancement

#61 - Question: extract haplotypes

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

#60 - genome-wide vs gene-sepecific pN/pS

Issue - State: closed - Opened by Thexiyang almost 4 years ago - 6 comments

#58 - allele frequency

Issue - State: closed - Opened by Thexiyang almost 4 years ago - 12 comments

#57 - No genomes detected

Issue - State: closed - Opened by samlipworth almost 4 years ago - 2 comments

#56 - Error running inStrain when including a genes file

Issue - State: closed - Opened by EvolDoc almost 4 years ago - 30 comments

#55 - inStrain profile issue with BAM format

Issue - State: closed - Opened by cswift3 almost 4 years ago - 3 comments

#54 - instrain compare: dynamic output

Issue - State: closed - Opened by nick-youngblut almost 4 years ago - 2 comments

#50 - Is it possible to know the species/strain name

Issue - State: closed - Opened by Biofarmer almost 4 years ago - 35 comments

#44 - position in gene for reverse strand

Issue - State: closed - Opened by ecvanderwijk almost 4 years ago - 5 comments

#39 - added per-group processing for inStrain compare

Pull Request - State: open - Opened by nick-youngblut about 4 years ago - 3 comments

#32 - mutation type missing for intergenic regions

Issue - State: closed - Opened by ecvanderwijk about 4 years ago - 14 comments

#14 - inStrain compare not scaling

Issue - State: closed - Opened by nick-youngblut almost 5 years ago - 11 comments
Labels: enhancement