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
