From da9e89df2b0cd091aca30e039e54f3b1205bc8c3 Mon Sep 17 00:00:00 2001 From: Barbara Novak <19824106+bnovak32@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:33:01 -0700 Subject: [PATCH] Update GL-DPPD-7113.md Added missing UCSC tools to software table. --- .../GL-DPPD-7113.md | 32 ++++++++++--------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md b/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md index e4199cf2..780f087b 100644 --- a/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md +++ b/Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md @@ -66,21 +66,23 @@ Jonathan Galazka (GeneLab Project Scientist) # Software used |Program|Version|Relevant Links| -|:-----------|:------:|------:| -|FastQC | 0.12.0 |[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)| -|MultiQC | 1.22.1 |[https://multiqc.info/](https://multiqc.info/)| -|Cutadapt | 4.8 |[https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable/)| -|TrimGalore! | 0.6.7 |[https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)| -|Bismark | 0.24.2 |[https://github.com/FelixKrueger/Bismark](https://github.com/FelixKrueger/Bismark)| -|bowtie2 | 2.5.4 |[https://github.com/BenLangmead/bowtie2#overview](https://github.com/BenLangmead/bowtie2#overview)| -|hisat2 | 2.2.1 |[https://github.com/DaehwanKimLab/hisat2](https://github.com/DaehwanKimLab/hisat2)| -|samtools | 1.20 |[https://github.com/samtools/samtools#samtools](https://github.com/samtools/samtools#samtools)| -|qualimap | 2.3 |[http://qualimap.conesalab.org/](http://qualimap.conesalab.org/)| -|R | 4.4.0 |[https://www.r-project.org](https://www.r-project.org)| -|tidyverse | 2.0.0 |[https://tidyverse.tidyverse.org/](https://tidyverse.tidyverse.org/)| -|Bioconductor| 3.19 |[https://bioconductor.org](https://bioconductor.org) -|methylKit | 1.30.0 |[https://bioconductor.org/packages/release/bioc/html/methylKit.html](https://bioconductor.org/packages/release/bioc/html/methylKit.html)| -|genomation | 1.36.0 |[https://bioconductor.org/packages/release/bioc/html/genomation.html](https://bioconductor.org/packages/release/bioc/html/genomation.html)| +|:------------|:------:|------:| +|FastQC | 0.12.0 |[https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)| +|MultiQC | 1.22.1 |[https://multiqc.info/](https://multiqc.info/)| +|Cutadapt | 4.8 |[https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable/)| +|TrimGalore! | 0.6.10 |[https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)| +|Bismark | 0.24.2 |[https://github.com/FelixKrueger/Bismark](https://github.com/FelixKrueger/Bismark)| +|bowtie2 | 2.5.4 |[https://github.com/BenLangmead/bowtie2#overview](https://github.com/BenLangmead/bowtie2#overview)| +|hisat2 | 2.2.1 |[https://github.com/DaehwanKimLab/hisat2](https://github.com/DaehwanKimLab/hisat2)| +|samtools | 1.20 |[https://github.com/samtools/samtools#samtools](https://github.com/samtools/samtools#samtools)| +|qualimap | 2.3 |[http://qualimap.conesalab.org/](http://qualimap.conesalab.org/)| +|gtfToGenePred| 447 |[http://hgdownload.cse.ucsc.edu/admin/exe/](http://hgdownload.cse.ucsc.edu/admin/exe/)| +|genePredToBed| 447 |[http://hgdownload.cse.ucsc.edu/admin/exe/](http://hgdownload.cse.ucsc.edu/admin/exe/) +|R | 4.4.0 |[https://www.r-project.org](https://www.r-project.org)| +|tidyverse | 2.0.0 |[https://tidyverse.tidyverse.org/](https://tidyverse.tidyverse.org/)| +|Bioconductor | 3.19 |[https://bioconductor.org](https://bioconductor.org) +|methylKit | 1.30.0 |[https://bioconductor.org/packages/release/bioc/html/methylKit.html](https://bioconductor.org/packages/release/bioc/html/methylKit.html)| +|genomation | 1.36.0 |[https://bioconductor.org/packages/release/bioc/html/genomation.html](https://bioconductor.org/packages/release/bioc/html/genomation.html)| ---