Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • UCSC mm10 gtf file

    Hi,
    I have dowloaded UCSC hg19 gtf files from Galaxy



    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????

  • #2
    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.

    Comment


    • #3
      Hi heso,

      The format of the file you downloaded from Galaxy looks like
      the iGenomes files.

      Comment


      • #4
        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

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X