From 885f7ae3441db4d70c160e5cab71c9670cd3be22 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Tue, 7 Apr 2020 14:19:11 +0200 Subject: [PATCH 1/4] added bs_pe_4a.html (cherry picked from commit 64283b3981eb3722ec994dd3f7bc9eb414f30249) --- bs_pe_4a.html | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 bs_pe_4a.html diff --git a/bs_pe_4a.html b/bs_pe_4a.html new file mode 100644 index 0000000..413f9c1 --- /dev/null +++ b/bs_pe_4a.html @@ -0,0 +1,67 @@ + + + + + + Bismark + + +

Bismark

+ + +

Description:

+

+Bismark analyses BS-Seq data by performing both read mapping and +methylation calling in a single run. Its output distinguishes between cytosines +in CpG, CHG and CHH contexts, and enables the visualization and interpretation +of the provided methylated data. +

+

Reference:

+ Bismark + + + From 0af9ae3f692628dfdc7cdcceabb569a3d0620b1d Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Tue, 7 Apr 2020 14:11:57 +0200 Subject: [PATCH 2/4] added bs_pe_5a.html (cherry picked from commit 0944a938b6b41477997ccc64e6d95a6c8c3d8c83) --- bs_pe_5a.html | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 bs_pe_5a.html diff --git a/bs_pe_5a.html b/bs_pe_5a.html new file mode 100644 index 0000000..ef48051 --- /dev/null +++ b/bs_pe_5a.html @@ -0,0 +1,70 @@ + + + + + + Samtools and MethylDackel + + +

Samtools and MethylDackel

+ + +

Description:

+

+Samtools is a library of utilities for post-processing alignments in the +SAM format, e.g indexing, variant calling and alignment viewing.
+
+MethylDackel processes coordinate-sorted and indexed BAM/CRAM files that +contain BS-Seq alignments, and extracts per-base methylation metrics. +MethylDackel also requires an indexed reference genome in the FASTA format. +

+

Reference:

+ Samtools + MethylDackel + + + From 28c4f0f97c4ad33ce2113906ccc81b07a6b09c38 Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Tue, 7 Apr 2020 15:07:18 +0200 Subject: [PATCH 3/4] added missing tools in the header --- bs_pe_5a.yaml | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/bs_pe_5a.yaml b/bs_pe_5a.yaml index cc8e14c..c823ae0 100644 --- a/bs_pe_5a.yaml +++ b/bs_pe_5a.yaml @@ -5,10 +5,17 @@ title_default: 'BS-Seq analysis (paired-end reads)' steps: - title: 'Outline' element: '#masthead:visible' - content: 'In this tour we will infer genome-wide methylation rates in a CpG context.
-Here, we will leverage on two tools:
-- Samtools, to extract uniquely mapped and properly paired sequences from aligned input data and mark duplicons
-- MethylDackel to quantify the methylated reads of the provided CpG context file.' + content: 'In this tour we will infer genome-wide methylation rates in a CpG +context.
+Here, we will leverage on:
+- Samtools, to extract uniquely mapped and properly paired sequences +from aligned input data and mark duplicons
+- MethylDackel, to quantify the methylated reads of the provided CpG +context file.
+- Bedtools, to extract the CpG methylation of potential promoters and +calculate mean methylation levels
+- Join, to join files on a shared column of values
+- AWK, to parse and extract table columns depending on their values.' placement: bottom From 99c2128bc4be9c558ef46a26deb1ac943fd0a36b Mon Sep 17 00:00:00 2001 From: Andrea Bagnacani Date: Tue, 7 Apr 2020 15:07:36 +0200 Subject: [PATCH 4/4] added missing tools in the description section --- bs_pe_5a.html | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/bs_pe_5a.html b/bs_pe_5a.html index ef48051..3a0e131 100644 --- a/bs_pe_5a.html +++ b/bs_pe_5a.html @@ -21,10 +21,10 @@ - Samtools and MethylDackel + Samtools, MethylDackel, Bedtools, Join and AWK -

Samtools and MethylDackel

+

Samtools, MethylDackel, Bedtools, Join and AWK