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Old 11-16-2014, 03:14 AM   #1
heso
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Location: Sweden

Join Date: May 2014
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Question UCSC mm10 gtf file

Hi,
I have dowloaded UCSC hg19 gtf files from Galaxy

https://usegalaxy.org/library_common...ccf9e20303b392

The resulting file looks like that:
$ head hg19_genes.gtf
Code:
chr1	unknown	exon	11874	12227	.	+	.	gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523";
chr1	unknown	exon	12613	12721	.	+	.	gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523";
chr1	unknown	exon	13221	14408	.	+	.	gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523";
chr1	unknown	exon	14362	14829	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	14970	15038	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	15796	15947	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	16607	16765	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	16858	17055	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	17233	17368	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";
chr1	unknown	exon	17606	17742	.	-	.	gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";

When obtaining the same file from UCSC Tables, the file looks somewhat different. First 3 rows are similar and thereafter things don't exactly match.....

$ head hg19_ucsc_table.gtf
Code:
chr1	hg19_knownGene	exon	11874	12227	0.000000	+	.	gene_id "uc001aaa.3"; transcript_id "uc001aaa.3"; 
chr1	hg19_knownGene	exon	12613	12721	0.000000	+	.	gene_id "uc001aaa.3"; transcript_id "uc001aaa.3"; 
chr1	hg19_knownGene	exon	13221	14409	0.000000	+	.	gene_id "uc001aaa.3"; transcript_id "uc001aaa.3"; 
chr1	hg19_knownGene	exon	11874	12227	0.000000	+	.	gene_id "uc010nxr.1"; transcript_id "uc010nxr.1"; 
chr1	hg19_knownGene	exon	12646	12697	0.000000	+	.	gene_id "uc010nxr.1"; transcript_id "uc010nxr.1"; 
chr1	hg19_knownGene	exon	13221	14409	0.000000	+	.	gene_id "uc010nxr.1"; transcript_id "uc010nxr.1"; 
chr1	hg19_knownGene	start_codon	12190	12192	0.000000	+	.	gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; 
chr1	hg19_knownGene	CDS	12190	12227	0.000000	+	0	gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; 
chr1	hg19_knownGene	exon	11874	12227	0.000000	+	.	gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; 
chr1	hg19_knownGene	CDS	12595	12721	0.000000	+	1	gene_id "uc010nxq.1"; transcript_id "uc010nxq.1";

So, when I grep out miRNA genes from the first gtf file obtained through Galaxy (hg19_genes.gtf ), I get a gtf file with only miRNA genes.
command:
Code:
$cat hg19_genes.gtf | grep "MIR" > hg19_miRNA.gtf
this command, however, does not work for the file I got from UCSC Tables (hg19_ucsc_table.gtf ). I guess the gene_id's are just denoted to contain miR/MIR symbol.

So, my question:
I would like to obtain miRNA gtf files for mm10 in UCSC format (I've used UCSC mm10 for mapping).
In Galaxy, there is only UCSC mm9 gtf file (https://usegalaxy.org/library_common...9490a8b6c89961).
How can I obtain UCSC mm10.gtf in a format, where I could grep out the miRNA genes????
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Old 11-16-2014, 04:24 AM   #2
GenoMax
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You can use the table browser at UCSC to export mm10 annotation in GTF format.

If you happen to have access to iGenomes mm10 download http://support.illumina.com/sequenci...e/igenome.html the GTF file would be in Annotations sub-directory.
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Old 11-16-2014, 12:12 PM   #3
mastal
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Posts: 667
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Hi heso,

The format of the file you downloaded from Galaxy looks like
the iGenomes files.
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Old 11-17-2014, 12:57 AM   #4
heso
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Location: Sweden

Join Date: May 2014
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I got it fixed now. I used this site for downloading.
ftp://ussd-ftp.illumina.com/Mus_musculus/UCSC/mm10/

There I found the gtf in the format I wanted.
Thanks everybody
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