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faq [2021/06/28 23:22]
ivan
faq [2021/06/28 23:26] (current)
ivan
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   NP_005792 110 V I   NP_005792 110 V I
  
-:!: Only UniProtKB protein accessions or entry names (eg. ''Q5UAW9'' or ''GP157_HUMAN'') are fully supported; RefSeq protein identifiers while supported may result in sequence errors due to high level of ambiguity in protein mappings. See Sample Query on the [[/pph2/bgi.shtml|Batch query]] web page for more examples of the supported query formats.+:!: Only UniProtKB protein accessions or entry names (eg. ''Q5UAW9'' or ''GP157_HUMAN'') are fully supported; RefSeq protein identifiers while supported may result in sequence errors due to high level of ambiguity in protein mappings. See Sample Query on the [[http://genetics.bwh.harvard.edu/pph2/bgi.shtml|Batch query]] web page for more examples of the supported query formats.
  
 ''**NOTIFYME**'' parameter is optional. If present, notification will be sent via e-mail address provided as its value upon batch completion. ''**NOTIFYME**'' parameter is optional. If present, notification will be sent via e-mail address provided as its value upon batch completion.
  
-Other optional parameters are listed below with their default values (matching [[/pph2/bgi.shtml|Batch query]] settings) highlighted in bold:+Other optional parameters are listed below with their default values (matching [[http://genetics.bwh.harvard.edu/pph2/bgi.shtml|Batch query]] settings) highlighted in bold:
  
 ''**MODELNAME**=**HumDiv**|HumVar'' - Classifier model used for predictions. ''**MODELNAME**=**HumDiv**|HumVar'' - Classifier model used for predictions.
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 ''**SNPFILTER**=0|**1**|3'' - Set of transcripts on which genomic SNPs will be mapped (0 - All, 1 - **Canonical**, 3 - CCDS). ''**SNPFILTER**=0|**1**|3'' - Set of transcripts on which genomic SNPs will be mapped (0 - All, 1 - **Canonical**, 3 - CCDS).
  
-''**SNPFUNC**=c|**m**'' - Functional SNP categories to include in genomic SNPs annotation report (''pph2-snps.txt'' file); leaving this parameter out or specifying empty value (e.g.: ''**SNPFUNC**='') will result in annotations reported for all SNP categories, same as selecting **Annotations->All** option on the [[/pph2/bgi.shtml|Batch query]] web page.+''**SNPFUNC**=c|**m**'' - Functional SNP categories to include in genomic SNPs annotation report (''pph2-snps.txt'' file); leaving this parameter out or specifying empty value (e.g.: ''**SNPFUNC**='') will result in annotations reported for all SNP categories, same as selecting **Annotations->All** option on the [[http://genetics.bwh.harvard.edu/pph2/bgi.shtml|Batch query]] web page.
  
-For detailed description of these parameters please go to [[/pph2/bgi.shtml|Batch query]] page and hover mouse pointer over corresponding option labels under **Advanced Options** section.+For detailed description of these parameters please go to [[http://genetics.bwh.harvard.edu/pph2/bgi.shtml|Batch query]] page and hover mouse pointer over corresponding option labels under **Advanced Options** section.
  
 If you want to submit your own set of protein sequences together with your query you will need to add the following extra ''-F'' option to your ''curl'' command line: If you want to submit your own set of protein sequences together with your query you will need to add the following extra ''-F'' option to your ''curl'' command line:
faq.txt · Last modified: 2021/06/28 23:26 by ivan