Changes between Version 1 and Version 2 of net.sf.basedb.reggie/notes415

Timestamp:

Feb 8, 2018, 1:49:33 PM (7 years ago)

Author:

Nicklas Nordborg

Comment:

Adding more update notes related to #1009, #1015, #1016 and #1018

net.sf.basedb.reggie/notes415

@@ -13 +13 @@
 
 Create a new software and protocol item for the !StringTie pipeline. They should have `Type=Feature extraction` and `ExpressionType=StringTie`. Keep the `Add as project default` checkbox checked and the `Replace existing default` unchecked.
+
+=== Create a new array design ===
+
+A new array design should be created for representing the data generated by the !StringTie step. The array design should have `Platform=Sequencing/StringTie`. Upload the GTF file (''gencode.v27.primary_assembly.annotation_subset_transcripttype_proteincoding.gtf'') that !StringTie uses and attach is as the `GTF ref-seq` file to the new array design. Note! It may take a while to save due to parsing the GTF file. Please be patient!
+
+=== Remove existing Hisat alignments ===
+
+Existing Hisat alignments should be removed. There is no masking step before the alignment, and the genotyping is done with a shorter list (51) SNPs. Do not attempt to run the "Genotype quality control" wizard before the old alignments have been removed since this may lead to unpredictable results.
+
+=== The QC_GenoTypeHET annotation type is no longer used ===
+
+The `QC_GenoTypeHET` annotation type has been replaced with `QC_GenoTypeHET_PCT`. Once all alignments that uses this annotation has been deleted the annotation type can be removed.