Genes in gtf or gff format: Revision history

5 February 2020

• curprev 00:0400:04, 5 February 2020‎ Lrnassar talk contribs‎ 22,997 bytes +179‎ No edit summary

4 February 2020

• curprev 19:1819:18, 4 February 2020‎ Dschmelt talk contribs‎ 22,818 bytes +418‎ Adding note about GTF downloads directory #20867

9 April 2019

• curprev 23:2123:21, 9 April 2019‎ Dschmelt talk contribs‎ 22,400 bytes −1,219‎ →‎The opposite direction, GTF to GenePred: Fixing chrom number
• curprev 23:1023:10, 9 April 2019‎ Dschmelt talk contribs‎ 23,619 bytes +797‎ →‎The opposite direction, GTF to GenePred: Fixing broken links in example

19 November 2018

• curprev 18:5118:51, 19 November 2018‎ Dschmelt talk contribs‎ 22,822 bytes +30‎ →‎Using kent commands with the public database server: Slight wording modifications.

16 November 2018

• curprev 22:1622:16, 16 November 2018‎ Dschmelt talk contribs‎ 22,792 bytes +45‎ →‎Using kent commands with the public database server: Ordering lines
• curprev 22:0822:08, 16 November 2018‎ Dschmelt talk contribs‎ 22,747 bytes +146‎ →‎Using kent commands with the public database server: Making more copy paste friendly.
• curprev 22:0422:04, 16 November 2018‎ Dschmelt talk contribs‎ 22,601 bytes +10‎ →‎Using kent commands with the public database server: Small typo edits
• curprev 21:4421:44, 16 November 2018‎ Dschmelt talk contribs‎ 22,591 bytes +15‎ →‎Using kent commands with the public database server: Adding few lines about downloading utility and setting permissions.
• curprev 21:3521:35, 16 November 2018‎ Dschmelt talk contribs‎ 22,576 bytes −1‎ →‎Using kent commands with the public database server: Formatting
• curprev 21:3521:35, 16 November 2018‎ Dschmelt talk contribs‎ 22,577 bytes −1‎ →‎Using kent commands with the public database server: Specifying path

1 September 2018

• curprev 07:5407:54, 1 September 2018‎ Galt talk contribs‎ 22,578 bytes 0‎ changed cse to soe

25 January 2018

• curprev 22:1322:13, 25 January 2018‎ Chmalee talk contribs‎ m 22,578 bytes +1‎ →‎Example with downloaded refGene.txt.gz: Adding 'n' to sort command to get numeric sort. Otherwise something like 10002682 will come before 11869
• curprev 00:3100:31, 25 January 2018‎ Cath Tyner talk contribs‎ 22,577 bytes +2,187‎ Adding example for perl script to replace the "gene ID" with the Ensembl ID, which is named "transcript_id."

22 December 2017

• curprev 17:2017:20, 22 December 2017‎ Cath Tyner talk contribs‎ m 20,390 bytes +209‎ No edit summary

31 October 2017

• curprev 23:1923:19, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,181 bytes +313‎ →‎Warning - using a non genePred table to get GTF output in the Table Browser
• curprev 22:5822:58, 31 October 2017‎ Cath Tyner talk contribs‎ m 19,868 bytes +107‎ →‎Summary of limitations for Table Browser GTF output
• curprev 22:5122:51, 31 October 2017‎ Cath Tyner talk contribs‎ m 19,761 bytes −401‎ →‎Warning - using a non genePred table to get GTF output in the Table Browser
• curprev 22:1822:18, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,162 bytes +35‎ →‎Warning - using a non genePred table to get GTF output in the Table Browser
• curprev 22:0722:07, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,127 bytes −1‎ →‎Warning - using a non genePred table to get GTF output in the Table Browser
• curprev 22:0622:06, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,128 bytes −7‎ →‎Summary of limitations for Table Browser GTF output
• curprev 22:0522:05, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,135 bytes +10‎ No edit summary
• curprev 22:0522:05, 31 October 2017‎ Cath Tyner talk contribs‎ m 20,125 bytes +1,992‎ No edit summary
• curprev 21:4021:40, 31 October 2017‎ Cath Tyner talk contribs‎ m 18,133 bytes +185‎ →‎Summary of limitations for Table Browser GTF output

4 October 2017

• curprev 16:2516:25, 4 October 2017‎ Chmalee talk contribs‎ 17,948 bytes +1‎ →‎The opposite direction, GTF to GenePred
• curprev 16:2416:24, 4 October 2017‎ Chmalee talk contribs‎ m 17,947 bytes +3,200‎ Adding a new section about going the other direction gtfToGenePred

14 August 2017

• curprev 19:5019:50, 14 August 2017‎ Brian Lee talk contribs‎ 14,747 bytes −2‎ →‎Mailing List Resources about GTF
• curprev 19:4919:49, 14 August 2017‎ Brian Lee talk contribs‎ 14,749 bytes +525‎ Adding some example connections to the MLQ where we have a lot of resources.

10 August 2017

• curprev 21:5121:51, 10 August 2017‎ Cath Tyner talk contribs‎ m 14,224 bytes +29‎ →‎Get a genePred file from UCSC MySQL public databases, then convert to GTF
• curprev 21:5021:50, 10 August 2017‎ Cath Tyner talk contribs‎ m 14,195 bytes −111‎ →‎Get a genePred file from UCSC MySQL public databases, then convert to GTF
• curprev 21:4921:49, 10 August 2017‎ Cath Tyner talk contribs‎ 14,306 bytes +397‎ →‎Get a genePred file from UCSC MySQL public databases, then convert to GTF
• curprev 21:4721:47, 10 August 2017‎ Cath Tyner talk contribs‎ 13,909 bytes +1,392‎ No edit summary

8 August 2017

• curprev 20:0720:07, 8 August 2017‎ Cath Tyner talk contribs‎ m 12,517 bytes −2‎ →‎Example to compare Table Browser GTF output with genePredToGtf utility output
• curprev 18:2918:29, 8 August 2017‎ Cath Tyner talk contribs‎ m 12,519 bytes +14‎ →‎Summary of limitations for Table Browser GTF output
• curprev 18:2818:28, 8 August 2017‎ Cath Tyner talk contribs‎ m 12,505 bytes −26‎ →‎Summary of limitations for Table Browser GTF output
• curprev 18:2618:26, 8 August 2017‎ Cath Tyner talk contribs‎ 12,531 bytes +464‎ No edit summary
• curprev 18:1718:17, 8 August 2017‎ Cath Tyner talk contribs‎ 12,067 bytes +4,446‎ Adding TB vs utility example

15 June 2017

• curprev 22:4022:40, 15 June 2017‎ Chmalee talk contribs‎ m 7,621 bytes +254‎ →‎Using kent commands with the public database server: adding note about matching gene_id and transcript_id when using knownGene table as input

17 March 2017

• curprev 21:3021:30, 17 March 2017‎ Brian Lee talk contribs‎ 7,367 bytes +35‎ →‎Use genePredToGtf with a downloaded genePred table: edit to suggest named subsection to enable link
• curprev 21:0221:02, 17 March 2017‎ Brian Lee talk contribs‎ 7,332 bytes +4‎ →‎Using Table Browser output as input for the genePredToGtf: correcting mention of GTF as input to genPredToGtf where it should be genPred
• curprev 20:3820:38, 17 March 2017‎ Cath Tyner talk contribs‎ 7,328 bytes −20‎ →‎Using Table Browser output as input for the genePredToGtf command line utility
• curprev 20:3820:38, 17 March 2017‎ Cath Tyner talk contribs‎ 7,348 bytes +83‎ No edit summary
• curprev 20:3720:37, 17 March 2017‎ Cath Tyner talk contribs‎ 7,265 bytes +2‎ →‎Convert genePred to GTF with the genePredToGtf command line utility
• curprev 20:3720:37, 17 March 2017‎ Cath Tyner talk contribs‎ 7,263 bytes +40‎ →‎Convert genePred to GTF with the genePredToGtf command line utility
• curprev 20:3620:36, 17 March 2017‎ Cath Tyner talk contribs‎ 7,223 bytes +286‎ →‎Bed format gene tracks (convert bed > genePred > GTF)
• curprev 20:3420:34, 17 March 2017‎ Cath Tyner talk contribs‎ 6,937 bytes −140‎ →‎Use genePredToGtf with a downloaded genePred table
• curprev 20:2120:21, 17 March 2017‎ Cath Tyner talk contribs‎ 7,077 bytes +27‎ →‎Convert genePred to GTF with the genePredToGtf command line utility
• curprev 20:2020:20, 17 March 2017‎ Cath Tyner talk contribs‎ 7,050 bytes −1‎ →‎Convert genePred to GTF with the genePredToGtf command line utility
• curprev 20:2020:20, 17 March 2017‎ Cath Tyner talk contribs‎ 7,051 bytes +85‎ →‎Convert genePred to GTF with the genePredToGtf command line utility

• curprev 20:1820:18, 17 March 2017‎ Cath Tyner talk contribs‎ 6,966 bytes 0‎ →‎Convert genePred to GTF with the genePredToGtf command line utility