Mercurial > repos > rhpvorderman > shm_csr
changeset 4:c8f02bce10d0 draft
"planemo upload commit 05326cc2233eb0fa8beaf4198bd7c1519f2a0bf9"
| author | rhpvorderman |
|---|---|
| date | Mon, 15 Nov 2021 14:04:10 +0000 |
| parents | dced6d52d218 |
| children | 495a521cf9f2 |
| files | shm_clonality.htm shm_csr.htm shm_csr.xml shm_downloads.htm shm_overview.htm shm_selection.htm shm_transition.htm utf8test.py |
| diffstat | 8 files changed, 25 insertions(+), 18 deletions(-) [+] |
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--- a/shm_clonality.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_clonality.htm Mon Nov 15 14:04:10 2021 +0000 @@ -88,7 +88,7 @@ name="OLE_LINK107"></a>Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. In<span class=apple-converted-space> </span><em>Bioinformatics, 31 (20), pp. -33563358.</em><span class=apple-converted-space><i> </i></span>[</span><a +3356–3358.</em><span class=apple-converted-space><i> </i></span>[</span><a href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span lang=EN-GB style='color:#303030'>doi:10.1093/bioinformatics/btv359</span></a><span lang=EN-GB style='color:black'>][</span><a
--- a/shm_csr.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_csr.htm Mon Nov 15 14:04:10 2021 +0000 @@ -49,7 +49,7 @@ style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The graphs in this tab give insight into the subclass distribution of IGG and IGA transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; -font-family:"Times New Roman","serif"'>Human C, Cα, Cγ and Cε +font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε constant genes are assigned using a </span><span lang=EN-GB style='font-size: 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script specifically designed for human (sub)class assignment in repertoire data as @@ -58,11 +58,11 @@ nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are then individually aligned in the right order to each input sequence. The percentage of the chunks identified in each rearrangement is calculated in the -chunk hit percentage. </span><span lang=EN-GB style='font-size:12.0pt; +‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; line-height:115%;font-family:"Times New Roman","serif"'>Cα and Cγ subclasses are very homologous and only differ in a few nucleotides. To assign subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: -115%;font-family:"Times New Roman","serif"'>nt hit percentage is calculated. +115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. This percentage indicates how well the chunks covering the subclass specific nucleotide match with the different subclasses. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
--- a/shm_csr.xml Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_csr.xml Mon Nov 15 14:04:10 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.2"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.3.2.1"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement>
--- a/shm_downloads.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_downloads.htm Mon Nov 15 14:04:10 2021 +0000 @@ -77,7 +77,7 @@ style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview -table as a data set. </span></p> +table as a data set. </span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per @@ -97,7 +97,7 @@ every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family: "Times New Roman","serif"'> links to a page showing for each transcript the sequence of the analysed region (as dependent on the sequence starts at filter), -the assigned subclass and the number of sequenced A,C,G and Ts.</span></p> +the assigned subclass and the number of sequenced A,C,G and T’s.</span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to @@ -135,7 +135,7 @@ generate the frequency by class plot:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows downloading the data used to generate frequency by class plot included in the -SHM frequency tab. </span></p> +SHM frequency tab. </span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for @@ -145,7 +145,7 @@ >20% SHM. Information is provided for each subclass.</span></p> <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif"'></span></p> +style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p> <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition @@ -267,7 +267,7 @@ <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB -style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the +style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the data used to generate the aa mutation frequency plot for all IGE sequences in the antigen selection tab.</span></p> @@ -314,7 +314,7 @@ data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Table output of the BASELINe analysis. Calculation of antigen selection as performed by BASELINe are shown for each individual IGG sequence and the sum of -all IGG sequences. </span></p> +all IGG sequences. </span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span @@ -373,7 +373,7 @@ style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'> Link to the overlap table as provided -under the clonality overlap tab. </span></p> +under the clonality overlap tab. </span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB @@ -388,7 +388,7 @@ style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt; font-family:"Times New Roman","serif"'> Gives a summary of the total number of -clones in all sequences and their clone size. </span></p> +clones in all sequences and their clone size. </span></p> <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB @@ -423,7 +423,7 @@ <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size: -12.0pt;font-family:"Times New Roman","serif"'>Downloads a table +12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the calculation of clonal relation between all IGM sequences. For each individual transcript the results of the clonal assignment as provided by Change-O are provided. Sequences with the same number in the CLONE column are
--- a/shm_overview.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_overview.htm Mon Nov 15 14:04:10 2021 +0000 @@ -49,7 +49,7 @@ settings chosen on the start page of the SHM & CSR pipeline and only include details on the analysed region as determined by the setting of the sequence starts at filter. All data in this table can be downloaded via the -downloads tab.</span></p> +“downloads” tab.</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Mutation
--- a/shm_selection.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_selection.htm Mon Nov 15 14:04:10 2021 +0000 @@ -55,7 +55,7 @@ color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying selection in high-throughput Immunoglobulin sequencing data sets. In<span class=apple-converted-space> </span><em>Nucleic Acids Research, 40 (17), -pp. e134e134.</em><span class=apple-converted-space><i> </i></span>[</span><span +pp. e134–e134.</em><span class=apple-converted-space><i> </i></span>[</span><span lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB @@ -94,7 +94,7 @@ PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>: focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The -custom boundries are dependent on the sequence starts at filter. </span></p> +custom boundries are dependent on the ‘sequence starts at filter’. </span></p> <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL style='font-family:UICTFontTextStyleBody;color:black'>Leader:
--- a/shm_transition.htm Mon Nov 15 11:35:18 2021 +0000 +++ b/shm_transition.htm Mon Nov 15 14:04:10 2021 +0000 @@ -82,7 +82,7 @@ "Times New Roman","serif"'>Heatmaps visualizing for each subclass the frequency of all possible substitutions. On the x-axes the original base is shown, while the y-axes shows the new base. The darker the shade of blue, the more frequent -this type of substitution is occurring. </span></a></p> +this type of substitution is occurring. </span></a></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Bargraph