Recent changes to annotation

annotation modified by Jin

Jin — Thu, 29 Sep 2016 14:48:26 -0000

--- v4
+++ v5
@@ -7,8 +7,8 @@
 b. Run the following commands:
 (1)gtfToGenePred -genePredExt -geneNameAsName2 Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.genePred
 (2) cut -f 1-10,12 Homo_sapiens.GRCh37.75.genePred > tmp.txt
-(3) echo -e "#GRCh37.ensGene.name\\tGRCh37.ensGene.chrom\\tGRCh37.ensGene.strand\\tGRCh37.ensGene.txStart\\tGRCh37.ensGene.txEnd\\tGRCh37.ensGene.cdsStart\\tGRCh37.ensGene.cdsEnd\\tGRCh37.ensGene.exonCount\\tGRCh37.ensGene.exonStarts\\tGRCh37.ensGene.exonEnds\\tGRCh37.ensemblToGeneName.value" > annot.enseml.GRCh37.txt
-(4) cat tmp.txt >> annot.enseml.GRCh37.txt
+(3) echo -e "#GRCh37.ensGene.name\\tGRCh37.ensGene.chrom\\tGRCh37.ensGene.strand\\tGRCh37.ensGene.txStart\\tGRCh37.ensGene.txEnd\\tGRCh37.ensGene.cdsStart\\tGRCh37.ensGene.cdsEnd\\tGRCh37.ensGene.exonCount\\tGRCh37.ensGene.exonStarts\\tGRCh37.ensGene.exonEnds\\tGRCh37.ensemblToGeneName.value" > annot.ensembl.GRCh37.txt
+(4) cat tmp.txt >> annot.ensembl.GRCh37.txt

 To use GRCh38/hg38, only an annotation file for GRCh38 and a reference file for GRCh38/hg38 need to be created or downloaded.

annotation modified by Jin

Jin — Thu, 14 Jul 2016 09:11:47 -0000

--- v3
+++ v4
@@ -1,9 +1,9 @@
 Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>, which contains the method of downloading annotation file for UCSC genes, Ensembl genes, Gencode genes, or RefSeq genes for INTEGRATE version 0.2.0 and previous versions.

-Since INTEGRATE version 0.2.5, the annotation file uses 11 columns. Two columns additional cdsStart and cdsEnd are added to the annotation file. Please refer to the ***annot.enseml.txt*** annotation file at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>  as an example. 
+Since INTEGRATE version 0.2.5, the annotation file uses 11 columns. Two additional columns cdsStart and cdsEnd are added to the annotation file. Please refer to the ***annot.enseml.txt*** annotation file at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>  as an example. 

 The above annotation file can also be created using a GTF file, for example:
-a. Download the gtf file at ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz.
+a. Download the GTF file at ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz.
 b. Run the following commands:
 (1)gtfToGenePred -genePredExt -geneNameAsName2 Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.genePred
 (2) cut -f 1-10,12 Homo_sapiens.GRCh37.75.genePred > tmp.txt

annotation modified by Jin

Jin — Thu, 14 Jul 2016 09:10:09 -0000

--- v2
+++ v3
@@ -1,4 +1,16 @@
-Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>
+Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>, which contains the method of downloading annotation file for UCSC genes, Ensembl genes, Gencode genes, or RefSeq genes for INTEGRATE version 0.2.0 and previous versions. 
+
+Since INTEGRATE version 0.2.5, the annotation file uses 11 columns. Two columns additional cdsStart and cdsEnd are added to the annotation file. Please refer to the ***annot.enseml.txt*** annotation file at <https: sourceforge.net="" projects="" integrate-fusion="" files=""/>  as an example. 
+
+The above annotation file can also be created using a GTF file, for example:
+a. Download the gtf file at ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz.
+b. Run the following commands:
+(1)gtfToGenePred -genePredExt -geneNameAsName2 Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRCh37.75.genePred
+(2) cut -f 1-10,12 Homo_sapiens.GRCh37.75.genePred > tmp.txt
+(3) echo -e "#GRCh37.ensGene.name\\tGRCh37.ensGene.chrom\\tGRCh37.ensGene.strand\\tGRCh37.ensGene.txStart\\tGRCh37.ensGene.txEnd\\tGRCh37.ensGene.cdsStart\\tGRCh37.ensGene.cdsEnd\\tGRCh37.ensGene.exonCount\\tGRCh37.ensGene.exonStarts\\tGRCh37.ensGene.exonEnds\\tGRCh37.ensemblToGeneName.value" > annot.enseml.GRCh37.txt
+(4) cat tmp.txt >> annot.enseml.GRCh37.txt
+
+To use GRCh38/hg38, only an annotation file for GRCh38 and a reference file for GRCh38/hg38 need to be created or downloaded.

annotation modified by Jin

Jin — Sat, 31 May 2014 05:27:02 -0000

--- v1
+++ v2
@@ -1,4 +1,4 @@
-Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at

+Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at

annotation modified by Jin

Jin — Sat, 31 May 2014 05:25:54 -0000

Please refer to Appendix A. Getting gene annotation file from UCSC Genome Browser at <>