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Index of /EvidentialGene/plants/cacao/relseq

      Name                                        Last modified       Size  

[DIR] Parent Directory 24-Oct-2022 23:07 - [TXT] cacao11genes_cir1nonalign.txt 12-Mar-2012 18:37 12k [   ] cacao11good_pub3i-cirad1c.gmap8.gff.gz 02-Mar-2012 23:01 10.1M [TXT] cacao11good_pub3i.ciradnonalign.ids 18-Mar-2012 17:15 115k [TXT] cacao11good_pub3i.ciradpoormap+nonalign.ids 11-Mar-2012 15:44 33k [TXT] cacao11good_pub3i.ciradpoormap-nonalign.ids 11-Mar-2012 15:44 17k [   ] cacao11good_pub3i.tr-cirad1c.gmap.out8g.gz 02-Mar-2012 22:49 15.5M [   ] cirad1cacao_gene1.tr-mars11.gmap.out8g.gz 19-Mar-2012 17:43 10.0M [   ] cirad_cacao1asm.nonalign.gff.gz 23-Aug-2011 15:53 82k [   ] ciradgene1-mars11.gmap8.gff.gz 19-Mar-2012 20:10 5.4M [TXT] ciradgene1.marspoormap+nonalign.ids 19-Mar-2012 20:30 5k [TXT] ciradgene1.marspoormap-nonalign.ids 19-Mar-2012 20:30 17k [TXT] ciradgene1.nonalignmars.ids 18-Mar-2012 18:22 13k [DIR] genestruc/ 21-Mar-2012 16:35 - [   ] mars_cacao11asm.nonalign.gff.gz 02-Mar-2012 22:12 279k


See ../docs/cacao11genes_cir1nonalign-work.txt for summaries from these data

Files of *.ids are gene ID lists for subsets of transcripts that do not map between assemblies

File name parts:
cacao11good_pub3i = Evigene version 3i gene set transcripts
ciradgene1 = Cirad version 1 gene set transcripts
ciradpoormap = transcripts map poorly (<90%) or not at all to cirad1 assembly
marspoormap = transcripts map poorly (<90%) or not at all to mars11 assembly
+nonalign = located in other assembly non-align spans (mars_cacao11asm.nonalign or cirad_cacao1asm.nonalign)
-nonalign = located outside of other assembly non-align spans

cacao11good_pub3i.ciradpoormap+nonalign.ids = Evigene transcripts that map poortly to cirad
      and also are in mars11 assembly non-align spans.
cacao11good_pub3i.ciradpoormap-nonalign.ids = same, but outside of non-align spans.
Likewise for ciradgene1.marspoormap..ids

IDs are derived from these data:
mars_cacao11asm.nonalign.gff  = mars assembly locations of non-alignment (gap) for asm x asm align
cirad_cacao1asm.nonalign.gff  = cirad assembly locations of non-align
cacao11good_pub3i-cirad1c.gmap8.gff = Evigene mars gene transcripts mapped to cirad assembly
ciradgene1-mars11.gmap8.gff   = cirad1 gene transcripts mapped to mars assembly


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Developed at the Genome Informatics Lab of Indiana University Biology Department