# Ordered list of annotations for the selection of Ensembl (coding, non-coding) associated to hCAGE data
# category_name	path_to_bed_6_file	Sense_or_AntiSense	Do_annotate	Do_filter	
# 1) TSS of coding and non_coding considered equally 
#    Annotate as "TSS,S"
TSS,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss.bed	S	1	-1
TSS,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss.bed	S	1	-1
#    Filter "TSS,S"
TSS,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss.bed	S	-1	1
TSS,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss.bed	S	-1	1
# 2) [-500..+500 or end of 1st exon] of coding and non_coding considered equally 
#    Annotate as "TSSregion500,S"
TSSregion500,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region500.bed	S	1	-1
TSSregion500,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region500.bed	S	1	-1
#    Filter TSSregion500,S
TSSregion500,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region500.bed	S	-1	1
TSSregion500,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region500.bed	S	-1	1
# 3-5) Remaining (not within [TSS..TSS+500 or end of 1st exon]) 5UTR of coding transcript in the order: first, inner and last
#      Annotate as "5UTR_first_exon,S"
#      Filter "5UTR_first_exon,S"
5UTR_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_5UTR.bed	S	1	1
#      Annotate as "5UTR_inner_exon,S"
#      Filter "5UTR_inner_exon,S"
5UTR_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_5UTR.bed	S	1	1
#      Annotate as "5UTR_last_exon,S"
#      Filter "5UTR_last_exon,S"
5UTR_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_5UTR.bed	S	1	1
# 6-9) Intron within the 5UTR of coding transcript in the order: first, inner and last
#      Annotate as "5UTR_first_intron,S"
#      Filter "5UTR_first_intron,S"
5UTR_first_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_5UTR.bed	S	1	1
#      Annotate as "5UTR_inner_intron,S"
#      Filter "5UTR_inner_intron,S"
5UTR_inner_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_5UTR.bed	S	1	1
#      Annotate as "5UTR_last_intron,S"
#      Filter "5UTR_last_intron,S"
5UTR_last_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_5UTR.bed	S	1	1
# 10) First exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_first_exon,S"
CDS_or_noncoding_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_CDS.bed	S	1	-1
CDS_or_noncoding_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_exon.bed	S	1	-1
#     Filter CDS_or_noncoding_first_exon,S
CDS_or_noncoding_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_CDS.bed	S	-1	1
CDS_or_noncoding_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_exon.bed	S	-1	1
# 11) Inner exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_inner_exon,S"
CDS_or_noncoding_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_CDS.bed	S	1	-1
CDS_or_noncoding_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_exon.bed	S	1	-1
#     Filter CDS_or_noncoding_inner_exon,S
CDS_or_noncoding_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_CDS.bed	S	-1	1
CDS_or_noncoding_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_exon.bed	S	-1	1
# 12) Last exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_last_exon,S"
CDS_or_noncoding_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_CDS.bed	S	1	-1
CDS_or_noncoding_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_exon.bed	S	1	-1
#     Filter CDS_or_noncoding_last_exon,S
CDS_or_noncoding_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_CDS.bed	S	-1	1
CDS_or_noncoding_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_exon.bed	S	-1	1
# 13-15) 3'UTR of coding transcript in the order: first, inner and last.
#        Annotate as "3UTR_first_exon,S"
#        Filter 3UTR_first_exon,S
3UTR_first_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_3UTR.bed	S	1	1
#        Annotate as "3UTR_inner_exon,S"
#        Filter 3UTR_inner_exon,S
3UTR_inner_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_3UTR.bed	S	1	1
#        Annotate as "3UTR_last_exon,S"
#        Filter 3UTR_last_exon,S
3UTR_last_exon,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_3UTR.bed	S	1	1
# 16) Antisense of TSS of coding and non_coding considered equally 
#     Annotate as "TSS,AS"
TSS,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss.bed	AS	1	-1
TSS,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss.bed	AS	1	-1
#     Filter TSS,AS
TSS,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss.bed	AS	-1	1
TSS,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss.bed	AS	-1	1
# 17) Antisense of [-500..+500 or end of 1st exon] of coding and non_coding considered equally 
#     Annotate as "TSSregion500,AS"
TSSregion500,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region500.bed	AS	1	-1
TSSregion500,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region500.bed	AS	1	-1
#     Filter TSSregion500,AS
TSSregion500,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region500.bed	AS	-1	1
TSSregion500,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region500.bed	AS	-1	1
# 18-21) Antisense of remaining (not within [TSS..TSS+500 or end of 1st exon]) 5UTR of coding transcript in the order: first, inner and last.
#        Annotate as "5UTR_first_exon,AS"
#        Filter 5UTR_first_exon,AS
5UTR_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_5UTR.bed	AS	1	1
#        Annotate as "5UTR_inner_exon,AS"
#        Filter 5UTR_inner_exon,AS
5UTR_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_5UTR.bed	AS	1	1
#        Annotate as "5UTR_last_exon,AS"
#        Filter 5UTR_last_exon,AS
5UTR_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_5UTR.bed	AS	1	1
# 22-25) Antisense of intron within the 5UTR of coding transcript in the order: first, inner and last
#        Annotate as "5UTR_first_intron,AS"
#        Filter 5UTR_first_intron,AS
5UTR_first_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_5UTR.bed	AS	1	1
#        Annotate as "5UTR_inner_intron,AS"
#        Filter 5UTR_inner_intron,AS
5UTR_inner_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_5UTR.bed	AS	1	1
#        Annotate as "5UTR_last_intron,AS"
#        Filter 5UTR_last_intron,AS
5UTR_last_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_5UTR.bed	AS	1	1
# 26) Antisense of first exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_first_exon,AS"
CDS_or_noncoding_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_CDS.bed	AS	1	-1
CDS_or_noncoding_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_exon.bed	AS	1	-1
#     Filter CDS_or_noncoding_first_exon,AS
CDS_or_noncoding_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_CDS.bed	AS	-1	1
CDS_or_noncoding_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_exon.bed	AS	-1	1
# 27) Antisense of  inner exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_inner_exon,AS"
CDS_or_noncoding_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_CDS.bed	AS	1	-1
CDS_or_noncoding_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_exon.bed	AS	1	-1
#     Filter CDS_or_noncoding_inner_exon,AS
CDS_or_noncoding_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_CDS.bed	AS	-1	1
CDS_or_noncoding_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_exon.bed	AS	-1	1
# 28) Antisense of last exon in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_last_exon,AS"
CDS_or_noncoding_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_CDS.bed	AS	1	-1
CDS_or_noncoding_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_exon.bed	AS	1	-1
#     Filter CDS_or_noncoding_last_exon,AS
CDS_or_noncoding_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_CDS.bed	AS	-1	1
CDS_or_noncoding_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_exon.bed	AS	-1	1
# 29-31) Antisense of 3'UTR of coding transcript in the order: first, inner and last
#        Annotate as "3UTR_first_exon,AS"
#        Filter 3UTR_first_exon,AS
3UTR_first_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_exon_in_3UTR.bed	AS	1	1
#        Annotate as "3UTR_inner_exon,AS"
#        Filter 3UTR_inner_exon,AS
3UTR_inner_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_exon_in_3UTR.bed	AS	1	1
#        Annotate as "3UTR_last_exon,AS"
#        Filter 3UTR_last_exon,AS
3UTR_last_exon,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_exon_in_3UTR.bed	AS	1	1
# 32) First intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_first_intron,S"
CDS_or_noncoding_first_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_CDS.bed	S	1	-1
CDS_or_noncoding_first_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_intron.bed	S	1	-1
#     Filter CDS_or_noncoding_first_intron,S
CDS_or_noncoding_first_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_CDS.bed	S	-1	1
CDS_or_noncoding_first_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_intron.bed	S	-1	1
# 33) Inner intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_inner_intron,S"
CDS_or_noncoding_inner_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_CDS.bed	S	1	-1
CDS_or_noncoding_inner_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_intron.bed	S	1	-1
#     Filter CDS_or_noncoding_inner_intron,S
CDS_or_noncoding_inner_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_CDS.bed	S	-1	1
CDS_or_noncoding_inner_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_intron.bed	S	-1	1
# 34) Last intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_last_intron,S"
CDS_or_noncoding_last_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_CDS.bed	S	1	-1
CDS_or_noncoding_last_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_intron.bed	S	1	-1
#     Filter CDS_or_noncoding_last_intron,S
CDS_or_noncoding_last_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_CDS.bed	S	-1	1
CDS_or_noncoding_last_intron,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_intron.bed	S	-1	1
# 35) Antisense of first intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_first_intron,AS"
CDS_or_noncoding_first_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_CDS.bed	AS	1	-1
CDS_or_noncoding_first_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_intron.bed	AS	1	-1
#     Filter CDS_or_noncoding_first_intron,AS
CDS_or_noncoding_first_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.first_intron_in_CDS.bed	AS	-1	1
CDS_or_noncoding_first_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.first_intron.bed	AS	-1	1
# 36) Antisense of  inner intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_inner_intron,AS"
CDS_or_noncoding_inner_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_CDS.bed	AS	1	-1
CDS_or_noncoding_inner_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_intron.bed	AS	1	-1
#     Filter CDS_or_noncoding_inner_intron,AS
CDS_or_noncoding_inner_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.inner_intron_in_CDS.bed	AS	-1	1
CDS_or_noncoding_inner_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.inner_intron.bed	AS	-1	1
# 37) Antisense of last intron in CDS of coding transcript or non-coding transcripts
#     Annotate as "CDS_or_noncoding_last_intron,AS"
CDS_or_noncoding_last_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_CDS.bed	AS	1	-1
CDS_or_noncoding_last_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_intron.bed	AS	1	-1
#     Filter CDS_or_noncoding_last_intron,AS
CDS_or_noncoding_last_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.last_intron_in_CDS.bed	AS	-1	1
CDS_or_noncoding_last_intron,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.last_intron.bed	AS	-1	1
# 38) [-1000..+1000 or end of 1st exon] (and that has not been previously filtered before) of coding and non_coding considered equally
#     Annotate as "upstreamTSS1000,S"
upstreamTSS1000,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region1000.bed	S	1	-1
upstreamTSS1000,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region1000.bed	S	1	-1
#     Filter upstreamTSS1000,S
upstreamTSS1000,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region1000.bed	S	-1	1
upstreamTSS1000,S	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region1000.bed	S	-1	1
# 39) Antisense of [-1000..+1000 or end of 1st exon] (and that has not been previously filtered before) of coding and non_coding considered equally
#     Annotate as "upstreamTSS1000,AS"
upstreamTSS1000,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region1000.bed	AS	1	-1
upstreamTSS1000,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region1000.bed	AS	1	-1
#     Filter upstreamTSS1000,AS
upstreamTSS1000,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.protein_coding.tss_region1000.bed	AS	-1	1
upstreamTSS1000,AS	CAGE-Tag-Cluster-Annotation-Data.ClosestTSS/mm9/UCSC_Ensembl_mm9_20120112.non_coding.tss_region1000.bed	AS	-1	1