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  • refseq vs gencode

    We are currently using refseq to do location analysis but we wish to switch to gencode.

    Old file: Human_hg19_refseq.txt
    Code:
    chr1	-	14362	29370	WASH5P	14362,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,	14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,
    chr1	-	34611	36081	FAM138A	34611,35276,35720,	35174,35481,36081,
    chr1	+	69090	70008	OR4F5	69090,	70008,
    chr1	+	367658	368595	OR4F16	367658,	368595,
    chr1	-	621097	622034	OR4F16	621097,	622034,
    chr1	-	761586	762902	NCRNA00115	761586,	762902,
    chr1	+	763063	789740	LOC643837	763063,764382,783033,787306,788050,788770,788956,	763155,764484,783186,787490,788146,788902,789740,
    chr1	-	803452	812182	FAM41C	803452,809491,812125,	804055,810535,812182,
    chr1	-	852952	854817	FLJ39609	852952,853401,854204,854714,	853100,853555,854295,854817,
    chr1	+	861120	879961	SAMD11	861120,861301,865534,866418,871151,874419,874654,876523,877515,877789,877938,878632,879077,879287,	861180,861393,865716,866469,871276,874509,874840,876686,877631,877868,878438,878757,879188,879961,
    chr1	-	879583	894679	NOC2L	879583,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,894594,	880180,880526,881033,881666,881925,883612,883983,886618,887519,887980,888668,889272,889462,891393,891595,892405,892653,894461,894679,
    chr1	+	895966	901095	KLHL17	895966,896672,897008,897205,897734,898083,898488,898716,899299,899486,899728,900342,	896180,896932,897130,897427,897851,898297,898633,898884,899388,899560,899910,901095,
    chr1	+	901876	910482	PLEKHN1	901876,902083,905656,905900,906065,906258,906456,906703,907454,907667,908240,908879,909212,909695,909821,	901994,902183,905803,905981,906138,906386,906588,906784,907530,907804,908390,909020,909431,909744,910482,
    chr1	-	910578	917473	C1orf170	910578,911878,914260,916516,917444,	911649,912004,916037,916553,917473,
    chr1	-	934341	935552	HES4	934341,934905,935071,935245,	934812,934993,935167,935552,
    chr1	-	934344	935552	HES4	934344,934905,935071,	934812,934993,935552,
    chr1	+	948846	949915	ISG15
    New file: gencode.v15.annotated.gtf
    Code:
    ##description: evidence-based annotation of the human genome (GRCh37), version 15 (Ensembl 70)
    ##provider: GENCODE
    ##contact: [email protected]
    ##format: gtf
    ##date: 2013-01-21
    chr1	HAVANA	gene	11869	14412	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
    chr1	HAVANA	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
    chr1	HAVANA	exon	11869	12227	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1;  level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
    chr1	HAVANA	exon	12613	12721	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2;  level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
    chr1	HAVANA	exon	13221	14409	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3;  level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
    chr1	ENSEMBL	transcript	11872	14412	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	11872	12227	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 1;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	12613	12721	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 2;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	13225	14412	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 3;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	transcript	11874	14409	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	11874	12227	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 1;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	12595	12721	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 2;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	13403	13655	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 3;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	ENSEMBL	exon	13661	14409	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 4;  level 3; havana_gene "OTTHUMG00000000961.2";
    chr1	HAVANA	transcript	12010	13670	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	12010	12057	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	12179	12227	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	12613	12697	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	12975	13052	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	13221	13374	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 5;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	exon	13453	13670	.	+	.	gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 6;  level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
    chr1	HAVANA	gene	14363	29806	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENSG00000227232.3"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P"; level 2; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	transcript	14363	29370	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	29321	29370	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 1;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	24738	24891	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 2;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	18268	18379	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 3;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	17915	18061	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 4;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	17602	17742	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 5;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	17233	17364	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 6;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	16854	17055	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 7;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	16607	16765	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 8;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	15904	15947	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 9;  level 3; havana_gene "OTTHUMG00000000958.1";
    chr1	ENSEMBL	exon	15796	15901	.	-	.	gene_id "ENSG00000227232.3"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 10;  level 3; havana_gene "OTTHUMG00000000958.1";
    Is this the correct correspondence?

    refseq column1=gencode column1 genelines only
    refseq column2=gencode column7 genelines only
    refseq column3=gencode column4 genelines only
    refseq column4=gencode column5 genelines only
    refseq column5=gencode column13 (gene name) genelines only
    refseq column6=gencode exon start columns
    refseq column7=gencode exon end columns

    I also assume both lists are in teh same order right? save one is more current?

  • #2
    Hi Jarwulf,

    the correspondence between two files is correct. Note that all Gencode coordinates are 1-based (actual genome position) whereas the Refseq gene and exon start coordinates are 0-based (you must add 1 to the coordinate to get the actual nucleotide position in the genome).

    The two files are sorted by chromosome and gene start, although in the Gencode file the exons on the negative strand are sorted from highest to lowest position, that is, from 5' to 3'.

    And, of course, the annotations are not the same between the two files!

    Hope this helps.

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