Mercurial > repos > davidvanzessen > shm_csr
comparison shm_csr.xml @ 47:64711f461c8e draft
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| author | davidvanzessen |
|---|---|
| date | Thu, 04 May 2017 07:43:09 -0400 |
| parents | a24f8c93583a |
| children | f5fe63533c58 |
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| 46:cfc9a442e59d | 47:64711f461c8e |
|---|---|
| 37 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" > | 37 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" > |
| 38 <option value="70_70" selected="true">>70% class and >70% subclass</option> | 38 <option value="70_70" selected="true">>70% class and >70% subclass</option> |
| 39 <option value="60_55">>60% class and >55% subclass</option> | 39 <option value="60_55">>60% class and >55% subclass</option> |
| 40 <option value="70_0">>70% class</option> | 40 <option value="70_0">>70% class</option> |
| 41 <option value="60_0">>60% class</option> | 41 <option value="60_0">>60% class</option> |
| 42 <option value="25_0">>25% class</option> | |
| 42 <option value="101_101">Do not assign (sub)class</option> | 43 <option value="101_101">Do not assign (sub)class</option> |
| 43 </param> | 44 </param> |
| 44 </conditional> | 45 </conditional> |
| 45 <conditional name="naive_output_cond"> | 46 <conditional name="naive_output_cond"> |
| 46 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> | 47 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> |
| 181 | 182 |
| 182 The SHM & CSR pipeline identifies human Cµ, Cα, Cγ and Cε constant genes by dividing the reference sequences for the subclasses (NG_001019) in 8 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are then individually aligned in the right order to each input sequence. This alignment is used to calculate the chunck hit percentage and the nt hit percentage. | 183 The SHM & CSR pipeline identifies human Cµ, Cα, Cγ and Cε constant genes by dividing the reference sequences for the subclasses (NG_001019) in 8 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are then individually aligned in the right order to each input sequence. This alignment is used to calculate the chunck hit percentage and the nt hit percentage. |
| 183 | 184 |
| 184 *Chunk hit percentage*: The percentage of the chunks that is aligned | 185 *Chunk hit percentage*: The percentage of the chunks that is aligned |
| 185 | 186 |
| 186 *Nt hit percentage*: The percentage of chunks covering the subclass specific nucleotide match with the different subclasses. The most stringent filter for the subclass is 70% ‘nt hit percentage’ which means that 5 out of 7 subclass specific nucleotides for Cα or 6 out of 8 subclass specific nucleotides of Cγ should match with the specific subclass. | 187 *Nt hit percentage*: The percentage of chunks covering the subclass specific nucleotide match with the different subclasses. The most stringent filter for the subclass is 70% ‘nt hit percentage’ which means that 5 out of 7 subclass specific nucleotides for Cα or 6 out of 8 subclass specific nucleotides of Cγ should match with the specific subclass. |
| 188 The option “>25% class” can be chosen when you only are interested in the class (Cα/Cγ/Cµ/Cɛ) of your sequences and the length of your sequence is not long enough to assign the subclasses. | |
| 187 | 189 |
| 188 ----- | 190 ----- |
| 189 | 191 |
| 190 **Output new IMGT archives per class into your history?** | 192 **Output new IMGT archives per class into your history?** |
| 191 | 193 |