Hello, Sushmita.
In GTF files, each exon has its own CDS record, but there is only one start and stop codon entry per gene. You will not see a start and stop codon entry for each individual CDS record. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group From: sushmita [mailto:[email protected]] Sent: Monday, June 25, 2012 5:56 AM To: [email protected] Cc: [email protected] Subject: Re: [Genome] Query related to liftOver tool Hi Steve, Thanks a lot for your co-operation. I understood "liftOver". I'll try to use that in my analysis. I have another doubt related to mouse (mm10) .gtf file. Here, I found that for each gene more than one CDSs were reported. As I know that, CDS codes protein, so it has start and stop codons. But, for eaxample: gene id "NM_175642" in mm10 .gtf file lots of CDSs are reported and only one start and stop codon. Could you please help me to understand that, what are those explaining. Following I am just pasting the records, which I got for this gene from the .gtf file. chr1 mm10_refGene stop_codon 25068168 25068170 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25068171 25068356 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25067476 25068356 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25074685 25074789 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25074685 25074789 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25084244 25084279 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25084244 25084279 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25093765 25094408 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25093765 25094408 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25098876 25098915 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25098876 25098915 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25101433 25101528 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25101433 25101528 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25111692 25111863 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25111692 25111863 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25112177 25112275 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25112177 25112275 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25117289 25117374 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25117289 25117374 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25126641 25126707 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25126641 25126707 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25128819 25128888 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25128819 25128888 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25131251 25131401 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25131251 25131401 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25221760 25221862 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25221760 25221862 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25226720 25226823 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25226720 25226823 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25228421 25228547 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25228421 25228547 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25396436 25396479 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25396436 25396479 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25420558 25420660 0.000000 - 1 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25420558 25420660 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25431423 25431498 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25431423 25431498 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25432427 25432576 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25432427 25432576 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25456992 25457100 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25456992 25457100 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25460743 25460811 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25460743 25460811 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25487925 25488119 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25487925 25488119 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25504433 25504539 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25504433 25504539 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25504913 25505014 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25504913 25505014 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25531870 25532034 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25531870 25532034 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25532475 25532639 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25532475 25532639 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25547416 25547580 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25547416 25547580 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25553675 25553836 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25553675 25553836 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25559755 25559865 0.000000 - 2 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25559755 25559865 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene CDS 25826004 25826760 0.000000 - 0 gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene start_codon 25826758 25826760 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25826004 25826775 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; chr1 mm10_refGene exon 25829462 25829707 0.000000 - . gene_id "NM_175642"; transcript_id "NM_175642"; Please help me to understand this. Thanks and Regards, Sushmita On 06/21/2012 12:54 AM, Steve Heitner wrote: Hello, Sushmita. If you are using the command line liftOver tool to convert mm9 genomic coordinates to mm10 genomic coordinates, then yes, you will use that file to perform the conversion. The basic usage of the liftOver tool is as follows: liftOver oldfile map.chain newfile unmapped oldfile: The file that contains your list of mm9 coordinates map.chain: The mm9ToMm10.over.chain file that you downloaded newfile: A target file that will contain the equivalent mm10 coordinates unMapped: A target file that contains any coordinates that could not be lifted over Please note that there is also a web-based liftOver tool that performs the same function and does not require you to download additional files. The web-based liftOver tool is located at http://genome.ucsc.edu/cgi-bin/hgLiftOver. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of sushmita Sent: Wednesday, June 20, 2012 5:26 AM To: [email protected] Subject: [Genome] Query related to liftOver tool Dear Sir/Madam, I downloaded "mm9ToMm10.over.chain" file from UCSC site. But the file content is not clear to me. Can you please help me to understand that? Shall I use this file to run "liftOver" tool? Thanks and Regards, Sushmita _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
