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  • trinity

    2020-11-29 20:01:29
    <div><p><strong>I try to install trinity by spack but face the error</strong></p> <pre><code> $ spack install trinity %gcc.4.0 ==> Error: An unsatisfiable version constraint has been ...
  • Trinity

    2021-01-02 16:11:08
    <div><ul>[x] I have read the <a href="https://bioconda.github.io/guidelines.html">...<p>Trinity bioconda update for version 2.8.1</p><p>该提问来源于开源项目:bioconda/bioconda-recipes</p></div>
  • TrinityTrinity漏洞-模拟器逃生
  • Rebuild trinity

    2020-12-30 06:36:13
    Recipe | <a href="https://github.com//bioconda/bioconda-recipes/tree/bump/trinity/recipes/trinity"><code>recipes/trinity</code></a> (click to view/edit other files) Releases |...
  • Dp trinity

    2020-12-09 02:27:11
    <div><p>Trinity now builds on linux (but not Mac), and test_tools succeeds on travis. I ran trinity's own test_Trinity_Assembly on my broad account and all tests passed. <p>I have NOT added a ...
  • Trinity Update

    2020-12-09 03:36:26
    <div><p>Please update changes: https://github.com/TrinityCore/TrinityCore/commit/ae3ab32ea5bf697a7b3f6d1fbc0740d7404d7c92</p> <p>thx.</p><p>该提问来源于开源项目:Shadez/wowarmory</p></div>
  • Trinity crash

    2020-11-25 23:02:23
    <p>Trinity crashed, logs are unclear as to why it shutdown. <p>...
  • Trinity Patch

    2020-12-09 02:20:14
    <div><p>Hey. What we do about trinity patch since it doesn't apply? Could you help us out please?!</p><p>该提问来源于开源项目:Shadez/wowarmory</p></div>
  • TrinityCore

    2012-05-13 15:46:23
    TrinityCore
  • 基于Debian的Trinity桌面环境。 Trinity是KDE 3的后继者。 在Docker中运行Trinity桌面。 使用在中运行GUI应用程序和桌面环境。 命令示例: 单个应用程序: x11docker x11docker/trinity konquerer 完整桌面: ...
  • TrinityCore (master) Build Status Introduction Requirements Install Reporting issues Submitting fixes Copyright Authors & Contributors Links Build Status master 3.3.5 ...
  • trinity bioinformatics

    2013-06-04 02:38:17
    Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many ...
  • add older Trinity

    2020-12-30 06:20:02
    <div><p>This adds a recipe for an older version of Trinity (2011-11-26) that uses an older assembly algorithm that works better with highly diverse viral genomes. It also restructures the regular ...
  • Trinity报错

    2019-09-25 13:16:59
    不管是用trinity的exmaple运行还是文献上提供的数据运行时,都会出现这样的错误,不知道是哪个软件没有安装好,还是哪里出错了。 转载于:https://www.cnblogs.com/ZHshuang463508120/p/3264081.html...

    不管是用trinity的exmaple运行还是文献上提供的数据运行时,都会出现这样的错误,不知道是哪个软件没有安装好,还是哪里出错了。

     

    转载于:https://www.cnblogs.com/ZHshuang463508120/p/3264081.html

    展开全文
  • Trinity package issues

    2020-12-30 06:27:22
    <div><p>We have an older version of trinity - 2011_11_26, which I believe is overriding the default latest versions in the 2.* series based on trinity version numbering. We need to figure out a new ...
  • ERROR ACCESING TRINITY

    2020-12-25 19:34:17
    <div><p>I download 1.4.2 for desktop windows 10. error migrating data. I download 1.4.3 for desktop windows 10. same error <p>I can't access my IOTA....iotaledger/trinity-wallet</p></div>
  • Error when building Trinity

    2020-12-08 19:25:32
    m trying to build Trinity with the help of wiki. When I run make, I get this error <code>make -C Switch/ext_snappy/ make[1]: Entering directory '/trinity-test/Trinity/Switch/ext_snappy' ar rc ...
  • 第一步建立文件夹在任意分区根目录建议一个文件夹,但是名称不要用中文,比如我在E盘建立文件夹Trinity.然后在文件夹Trinity右键选择Git Bash Here之后出现以下画面之后输入下载源码的命令:git clone -b 3.3.5 git:...

    第一步建立文件夹

    在任意分区根目录建议一个文件夹,但是名称不要用中文,比如我在E盘建立文件夹Trinity.

    然后在文件夹Trinity右键选择Git Bash Here

    之后出现以下画面

    6f98af49fbfb922c038639f70299ae72.png

    之后输入下载源码的命令:

    git clone -b 3.3.5 git://github.com/TrinityCore/TrinityCore.git

    db3b0cc30a965b6bf2fdc268422a5d2f.png

    然后回车等待源码下载

    完成后如下图

    2b89308319cd8f5aa577718c359376ee.png

    然后去E盘打开Trinity里面会多一个TrinityCore文件夹 这就里面是源码

    在Trinity文件夹下建立一个文件夹比如我是Core

    完成后如下图

    499ab845b8884415b1d04294c982c943.png

    运行桌面的CMake (cmake-gui)程序

    然后按照图片所示做对应选择

    b998391b0e6dd819a7748896cc9bdf56.png

    点击Configure 会弹出这个界面,如图所示选择

    3f720c47cb5844cb7813816307bf14da.png

    点击Finish继续

    等待软件输出结果

    第一次一般都会提示错误,错误的意思是你没有安装或指定mysql路径

    9904d9833bb668efdcfd81456a3a0390.png

    因为上个教程 说mysql是解压之后放着没懂的,所以这个里咱们给它指定以下对应路径

    点错误提示的 OK继续

    这里我们按照图片所示指定mysql对应路径

    9c1215c7ea1041e34ee904e03abd973c.png

    继续点击Configure就不会出现错误了

    edbaae3151492800a42ad3564ddbc580.png

    如下图一样就没有错了

    我们继续下一步

    点击Generate等待执行完毕后

    bec3b6c4f210aed032374d5b4b393fc1.png

    Open Project这个选项就可以点击了

    我们点击Open Project按钮进入VS2017进行下一步的编译操作

    这时候我们就和编译ACE一样的选择点击本地Windows调试模式 等待文件编译完成

    526ab32cf85b5f5cb2829b706aefe15f.png

    编译中截图如下

    a0e66325d01e942df7b509ee75f28224.png

    编译完成后截图如下

    4c60bbf538ad354cca368b378fdc0b6c.png

    然后我们进入E:\Trinity\Core\bin\Release就可以看到我们编译成功的TrinityCore端程序,还有地图提取程序,配置文件等。

    1c900e0a8af98b2eb6cc6c0495e8822c.png

    到这里TrinityCore程序就编译完成了。下一步来是建立数据库和修改配置文件来运行程序。

    展开全文
  • trinity.vim

    2014-03-30 23:24:13
    this is a controler of trinity of vim.
  • Update trinity to 2.8.5

    2020-12-30 09:14:48
    Recipe | <a href="https://github.com//bioconda/bioconda-recipes/tree/bump/trinity/recipes/trinity"><code>recipes/trinity</code></a> (click to view/edit other files) Releases |...
  • TrinityCore (3.3.5) Build Statusmaster3.3.5IntroductionTrinityCore is a MMORPG Framework based mostly in C++.It is derived from MaNGOS, the Massive Network Game Object Server, and isbased on the code....

    372162496429087fb0eea2443191f42d.png TrinityCore (3.3.5)

    TrinityCore.svgTrinityCore.svg

    Build Status

    master

    3.3.5

    TrinityCore.svg?branch=master

    TrinityCore.svg?branch=3.3.5

    master?svg=true

    3.3.5?svg=true

    badge.svg

    badge.svg

    Introduction

    TrinityCore is a MMORPG Framework based mostly in C++.

    It is derived from MaNGOS, the Massive Network Game Object Server, and is

    based on the code of that project with extensive changes over time to optimize,

    improve and cleanup the codebase at the same time as improving the in-game

    mechanics and functionality.

    It is completely open source; community involvement is highly encouraged.

    If you wish to contribute ideas or code please visit our site linked below or

    make pull requests to our Github repository.

    For further information on the TrinityCore project, please visit our project

    website at TrinityCore.org.

    Requirements

    Software requirements are available in the wiki for

    Windows, Linux and OS X.

    Install

    Detailed installation guides are available in the wiki for

    Windows, Linux and OS X.

    Reporting issues

    Issues can be reported via the Github issue tracker.

    Please take the time to review existing issues before submitting your own to

    prevent duplicates.

    In addition, thoroughly read through the issue tracker guide to ensure

    your report contains the required information. Incorrect or poorly formed

    reports are wasteful and are subject to deletion.

    Submitting fixes

    C++ fixes are submitted as pull requests via Github. For more information on how to

    properly submit a pull request, read the how-to: maintain a remote fork.

    For SQL only fixes open a ticket or if a bug report exists for the bug post on existing ticket.

    Copyright

    License: GPL 2.0

    Read file COPYING.

    Authors & Contributors

    Read file AUTHORS.

    Links

    展开全文
  • Trinity 一条龙策略

    2019-09-25 13:17:12
    1. Trinity进行转录组组装 Trinity进行转录组组装的典型命令如下: $ /opt/biosoft/trinityrnaseq_r20131110/Trinity.pl --seqType fq --JM 50G\ --left sample1_1.clean.fastq sample2_1.clean.fastq\ --...

    1. Trinity进行转录组组装

    Trinity进行转录组组装的典型命令如下:

    $ /opt/biosoft/trinityrnaseq_r20131110/Trinity.pl --seqType fq --JM 50G\
     --left sample1_1.clean.fastq sample2_1.clean.fastq\
     --right sample1_2.clean.fastq sample2_2.clean.fastq\
     --jaccard_clip --CPU 6 --SS_lib_type FR

    –JM后的参数设定与转录组的大小有关,在内存足够的情况下,设定大点能节约时间;
    –left 和 –right后可以接多个样平的数据,并用空格隔开,值得注意的是,left reads name以/1结尾,rigth reads name以/2结尾;
    –jaccard_clip 适合于基因稠密的真菌物种;
    –SS_lib_type 适合于链特异性测序

    大数据量(>300M pairs)的RNA-seq数据,最好使用TRINITY_RNASEQ_ROOT/util/normalize_by_kmer_coverage.pl对reads进行处理后再使用trinity进行组装,以降低内存消耗和大量时间。
    也可以设置–min_kmer_cov 2,丢弃uniquely occurring kmer, 从而降低内存消耗。

    参考文献:
    1. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. PubMed PMID: 21572440.
    2. Borodina T, Adjaye J, Sultan M. A strand-specific library preparation protocol for RNA sequencing. Methods Enzymol. 2011;500:79-98. PubMed PMID: 21943893.

    2. Trinity输出结果的统计

    Trinity默认的输出结果为:trinity_out_dir/Trinity.fasta。
    该fasta格式文件中序列名例如:

    >comp6749_c0_seq1 len=328 path=[471:0-83 388:84-208 679:209-327]
    >comp6749_c0_seq2 len=328 path=[304:0-83 388:84-208 679:209-327]
    >comp6749_c0_seq3 len=245 path=[901:0-125 679:126-244]
    

    可以看到,trinity生成的结果为components,而一个components可能有多个seq。这相当于一个gene能有多个transcripts。

    可以使用trinity自带的程序TrinityStats.pl对components和transcripts的数目,大小和N50等进行统计。

    $ $TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta
    Total trinity transcripts:	40138
    Total trinity components:	31067
    Percent GC: 61.31
    

     

    3. 将reads比对到转录组,并进行可视化

    TRINITY_RNASEQ_ROOT/util/alignReads.pl能调用bowtie将reads map到转录组,并可以设置链特异性参数。

    $ TRINITY_RNASEQ_ROOT/util/alignReads.pl --left left.fq --right right.fq --seqType fq\
     --target Trinity.fasta --aligner bowtie --retain_intermediate_files
    

    结果中生成coordSorted和nameSorted的sam和bam文件。如果设置了链特异性参数,则额外生成+链和-链的比对结果文件。

    TRINITY_RNASEQ_ROOT/util/SAM_nameSorted_to_uniq_count_stats.pl用于统计比对结果

    $ $TRINITY_HOME/util/SAM_nameSorted_to_uniq_count_stats.pl bowtie_out.nameSorted.sam.+.sam
    #read_type  count   pct
    proper_pairs    21194964    93.22    both read pairs align to a single contig and point toward each other.
    left_only   836213  3.68             only the left (/1) read is reported in an alignment
    right_only  687576  3.02             only the right (/2) read is reported in an alignment
    improper_pairs  16640   0.07         both left and right reads align, but to separate contigs, or to a single contig in the wrong expected relative orientations.
    

     

    可以将Trinity.fasta导入到IGV中作为genome,上载bam文件,从而可视化比对结果。

    4. 使用RSEM进行表达量计算

    首先,需要下载最新版本的RSEM,安装并将程序加入到$PATH中。

    $ wget http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.8.tar.gz
    $ tar zxf rsem-1.2.8.tar.gz
    $ cd rsem-1.2.8
    $ make
    $ echo "PATH=$PWD:\$PATH" >> ~/.bashrc
    

    使用$TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl可以调用RSEM,从而计算表达量。如果是链特异性测序,则加入–SS_lib_type参数。

    $TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta \
            --seqType fq --left left.reads.fq --right right.reads.fq --SS_lib_type FR \
            --prefix RSEM --thread_count 4 -- --bowtie-phred64-quals --no-bam-output
    

    将rsem-calculate-expression程序的参数–bowtie-phred64-quals和–no-bam-output加入到run_RSEM_align_n_estimate.pl中,则如上所示。这两个参数分别代表fastq的质量格式是phred64,不输出bam文件(节约大量时间)。
    若运行出现问题,点击:RSEM的README文件

    结果生成两个abundance estimation information文件:
    RSEM.isoforms.results : EM read counts per Trinity transcript
    RSEM.genes.results : EM read counts on a per-Trinity-component (aka… gene) basis, ‘gene’ used loosely here.

    可以根据得到的结果,去除掉IsoPct低于1%的transcripts。可以依据RSEM.isoforms.results使用TRINITY_RNASEQ_ROOT/util/filter_fasta_by_rsem_values.pl过滤掉trinity组装结果中的lowly supported transcripts。
    但不推荐过滤掉这些序列。

    5. 鉴定差异表达transcripts

    Trinity可以使用Bioconductor package中的edgeR或DESeq来鉴定差异表达trancripts。因此,需要安装R和相关的一些包。

    source("http://bioconductor.org/biocLite.R")
    biocLite('edgeR')
    biocLite('DESeq')
    biocLite('ctc')
    biocLite('Biobase')
    install.packages('gplots’)
    install.packages(‘ape’)
    

    5.1 使用上一节中的RSEM来分别对每个样品的每个生物学重复进行表达量计算

    5.2 将每个样的RSEM的结果进行合并

    $ $TRINITY_HOME/util/RSEM_util/merge_RSEM_frag_counts_single_table.pl \
    sampleA.RSEM.isoform.results sampleB.RSEM.isoform.results ... \
    > transcripts.counts.matrix
    $ TRINITY_HOME/util/RSEM_util/merge_RSEM_frag_counts_single_table.pl \
    sampleA.RSEM.gene.results sampleB.RSEM.gene.results ... \
    > genes.counts.matrix
    

    然后修改生成的两个matrix文件的column headers(代表着样品和重复的名字),有利于下游的分析。如果要分析transcripts水平的差异表达,则使用transcripts.counts.matrix文件;若要分析gene水平的差异表达,则使用genes.counts.matrix。

    5.3 无生物学重复进行差异表达分析

    $TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl用于调用edgeR或DESeq进行差异表达基因分析。直接输入该命令查看其用法。
    Trinty推荐使用edgeR进行差异表达分析。

    $TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl \
    --matrix counts.matrix --method edgeR
    

    注意输入的matrix是counts的数据,而不要是FPKM的数据。

    5.4 有生物学重复进行差异表达分析

    首先,要建立文件samples_described.txt,内容为:

    conditionA   condA-rep1
    conditionA   condA-rep2
    
    conditionB   condB-rep1
    conditionB   condB-rep2
    
    conditionC   condC-rep1
    conditionC   condC-rep2
    

    condA-rep1, condA-rep2, condB-rep1… 等对应着counts.matrix文件中的column names。
    命令如下:

    $TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl \
    --matrix SP2.rnaseq.counts.matrix --method edgeR \
    --samples_file samples_described.txt
    

    结果文件中 logFC 是 log2 Fold Change; logCPM 是 log2-counts-per-million。

    值得注意的是:程序默认去除counts数都少于10的transcripts或genes,不对其进行差异分析。所以有差异分析的genes或transcripts数目低于原始的数目。

    5.5 提取差异表达基因,对其进行聚类分析

    5.5.1 表达量的 NORMALIZED

    使用TMM方法将counts转换为FPKM。
    首先从1个样平的RSEM结果中提取长度数据:

    $ cut -f 1,3,4 sampleA.RSEM.isoforms.results > feature_lengths.txt
    

    然后使用TMM方法将counts数据转换为FPKM数据:

    $ $TRINITY_HOME/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl \
    --matrix counts.matrix --lengths feature_lengths.txt
    

    5.5.2 提取差异表达转录子

    注意的是,这一步要在edgeR的结果文件中运行程序:

    $ $TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl \
    --matrix matrix.TMM_normalized.FPKM -P 0.001 -C 2
    

    默认下选择FDR值低于0.001,log2fold-change的绝对值>=2为差异表达基因。
    程序输出差异表达基因FPKM、log2FC、FDR等值 和 聚类图 Heat Map.

    5.5.3 根据聚类图提取子类

    根据聚类结果,可以自动或手动确定子类。
    自动确定子类:

    $ $TRINITY_HOME/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl \
    --Ptree 20 -R file.all.RData
    

    上例中从数的20%处来自动划分子类。
    手动确定子类:

    $ R
    > load("all.RData") # check for your corresponding .RData file name to use here, replace all.RData accordingly
    > source("$TRINITY_HOME/Analysis/DifferentialExpression/R/manually_define_clusters.R")
    > manually_define_clusters(hc_genes, centered_data)
    然后左键点击选择子类,右键结束选择
    

    6. 提取蛋白编码区

    使用transdecoder从trinity的转录子中提取coding region。最新版的transdecoder貌似有点问题。

    $ $TRINITY_HOME/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl \
    -t transcripts.fasta -m 100
    

    默认下允许的最小的protein长度为100.
    提取出了coding region,得出对应的protein序列,有利于于下一步的功能注释。

     

    原文出自:http://www.chenlianfu.com/?p=2026

    转载于:https://www.cnblogs.com/ZHshuang463508120/p/3607933.html

    展开全文
  • Trinity: dev mode

    2020-12-27 16:11:46
    <div><p>I would like to propose and work on a dev mode implementation for Trinity (as mentioned in "Do soon" list at https://github.com/ethereum/py-evm/issues/816). I suggest to follow ganache...
  • <div><p>I have consulted the stars and it is time to cut the umbilical cord and move the <code>p2p</code> and <code>trinity</code> modules into the https://github.com/ethereum/trinity repository. ...
  • <ul><li>[ ] full sync</li><li>[ ] $ trinity</code><ul>[ ] initializes databases and runs full sync on main chain</li><li>[ ] starts with fast sync if local head is older than 24h, then switches to ...
  • Running Trinity

    千次阅读 2013-12-24 16:11:01
    Running Trinity Trinity is run via the script: Trinity.pl found in the base installation directory. Usage info is as follows: #######################################################...
  • Trinity long run Job

    2020-12-28 22:29:11
    <p>Now a new Circle CI job is created to run <code>trinity --ropsten</code> for 90 seconds. <h4>Cute Animal Picture <p><img alt="put a cute animal picture link inside the parentheses" src=...
  • trinity6.github.io-源码

    2021-03-10 10:21:04
    trinity6.github.io

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