Commit 1a2aaa79 authored by Steve Trevanion's avatar Steve Trevanion
Browse files

vega changes

parent 070a3f46
......@@ -100,23 +100,23 @@
31 fpc_clone_id fpc clone
# additional gene counts for Vega (see GeneCount for general description)
32 KnownPCCount protein_coding_KNOWN Number of Known Protein Coding
33 NovelPCCount protein_coding_NOVEL Number of Novel Protein Coding
34 NovelPTCount processed_transcript_NOVEL Number of Novel Processed Transcripts
32 KnwnPCCount protein_coding_KNOWN Number of Known Protein Coding
33 NovPCCount protein_coding_NOVEL Number of Novel Protein Coding
34 NovPTCount processed_transcript_NOVEL Number of Novel Processed Transcripts
35 PutPTCount processed_transcript_PUTATIVE Number of Putative Processed Transcripts
36 PredPCCount protein_coding_PREDICTED Number of Predicted Protein Coding
37 IgSegCount total_Ig_segment_UNKNOWN Number of Ig Segments
38 IgPsSegCount Ig_pseudogene_segment_UNKNOWN Number of Ig Pseudogene Segments
39 TotPsCount total_pseudogene_UNKNOWN Number of Pseudogenes
40 ProcPsCount processed_pseudogene_UNKNOWN Number of Processed pseudogenes
41 UnprocPsCount unprocessed_pseudogene_UNKNOWN Number of Unprocessed pseudogenes
42 KnwnPCProgCount protein_coding_in_progress_KNOWN Number of Known Protein coding genes in progress
43 NovPCProgCount protein_coding_in_progress_NOVEL Number of Novel Protein coding genes in progress
37 NovIgSegCount ig_segment Number of Novel Ig Segments
38 NovIgPsSegCount ig_pseudogene_segment Number of Novel Ig Pseudogene Segments
39 TotPsCount total_pseudogene Total Number of Pseudogenes
40 KnwnProcPsCount processed_pseudogene Number of Known Processed Pseudogenes
41 KnwnUnPsCount unprocessed_pseudogene Number of Known Unprocessed Pseudogenes
42 KnwnPCProgCount protein_coding_in_progress_KNOWN Number of Known Protein Coding in progress
43 NovPCProgCount protein_coding_in_progress_NOVEL Number of Novel Protein Coding in progress
# Vega annotation stats
44 AnnotSeqLength Annotated sequence length Total length of annotated clone sequence
45 TotCloneNum Total number of clones Total number of clones
46 NumAnnotClone Fully annotated clones Number of fully annotated clones
44 AnnotSeqLength Annotated sequence length Annotated Sequence
45 TotCloneNum Total number of clones Total Number of Clones
46 NumAnnotClone Fully annotated clones Number of Fully Annotated Clones
# Acknowledgements for manual annotation of this seq_region
47 ack Acknowledgement Acknowledgement for manual annotation
......@@ -132,7 +132,7 @@
53 author_email Author email address Author email address
54 remark Remark Annotation remark
55 transcr_class Transcript class Transcript class
56 KnownPTCount processed_transcript_KNOWN Number of Known Processed Transcripts
56 KnwnPTCount processed_transcript_KNOWN Number of Known Processed Transcripts
57 ccds CCDS CCDS identifier
# make first amino acid methionine
......@@ -223,10 +223,9 @@
# loutre attribs for vega production (st3)
130 vega_name Vega name Vega seq_region.name
131 vega_export_mod Export mode E (External), I (Internal) etc
131 vega_export_mode Export mode E (External), I (Internal) etc
132 vega_release Vega release Vega release number
# loutre attribs for assembly_tags (ck1)
133 atag_CLE Clone_left_end Clone_lef_end feature marked in GAP database
134 atag_CRE Clone_right_end Clone_right_end feature marked in GAP database
......@@ -253,3 +252,20 @@
#genebuild - databases of removed transcripts
146 kill_reason Kill Reason Reason why a transcript has been killed
147 strip_UTR Strip UTR Transcript needs bad UTR removing
# vega
148 TotAssLength Finished sequence length Finished Sequence
149 NovPsCount novel_pseudogene Number of Novel Pseudogenes
150 KnwnPsCount known_pseudogene Number of Known Pseudogenes
151 KnwnTPsCount known_transcribed_pseudogene Number of Known Transcribed Pseudogenes
152 TotPTCount total_processed_transcript Total Number of Processed Transcripts
153 TotPCCount total_protein_coding Total Number of Protein Coding
154 NovNcCount novel_non_coding Number of Novel Non Coding
155 KnwnPolyCount known_polymorphic Number of Known Polymorphic
156 NovPolyCount novel_polymorphic Number of Novel Polymorphic
157 TotIgSegCount total_ig_segment Total Number of Ig Segments
158 NovProcPsCount novel_processed_pseudogene Number of Novel Processed Pseudogenes
159 NovUnPsCount novel_unprocessed_pseudogene Number of Novel Unprocessed Pseudogenes
160 NovTPsCount novel_transcribed_pseudogene Number of Novel Transcribed Pseudogenes
161 NovTECCount novel_TEC Number of Novel TEC Genes
161 KnwnIgSegCount known_ig Number of Known Ig Segments
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