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  • reference sequence - splice sites

    Hi

    I'm just starting to work with NGS, and my first task is to prepare a reference sequence with splice sites. To do this I used the annotation table knownGene.txt from UCSC ftp server (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database). Reference sequence build is 36.1.

    I attach an example of extracted splice sites for first 10 genes from knownGene.txt annotation table, for 32 base pairs on each splice site.

    I would appreciate the information, if it is done properly and if not, what is wrong/missing.

    Thanks
    Attached Files

  • #2
    Originally posted by marada View Post
    Hi

    I'm just starting to work with NGS, and my first task is to prepare a reference sequence with splice sites. To do this I used the annotation table knownGene.txt from UCSC ftp server (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database). Reference sequence build is 36.1.

    I attach an example of extracted splice sites for first 10 genes from knownGene.txt annotation table, for 32 base pairs on each splice site.

    I would appreciate the information, if it is done properly and if not, what is wrong/missing.

    Thanks
    well i took a quick look at the last one (i'm usually fast to spot bugs -at least mines) and it looks suspicious to me..

    >chr1:8385-8417:8775-8807 strand: - name: uc009viu.1_8,
    ACGAACTTTTTAAGAGCACCTTCGCCGAGTCAagtaggaacgaagaaagttgtattttgtttaa

    If i go to the region chr1:8,386-8,417, i do not recognize any side from the sequence of the junction (nor the reverse complementary).
    Plus the sequence does not blat anywhere, which is suspicious too.

    Comment


    • #3
      Originally posted by steven View Post
      well i took a quick look at the last one (i'm usually fast to spot bugs -at least mines) and it looks suspicious to me..

      >chr1:8385-8417:8775-8807 strand: - name: uc009viu.1_8,
      ACGAACTTTTTAAGAGCACCTTCGCCGAGTCAagtaggaacgaagaaagttgtattttgtttaa

      If i go to the region chr1:8,386-8,417, i do not recognize any side from the sequence of the junction (nor the reverse complementary).
      Plus the sequence does not blat anywhere, which is suspicious too.

      Thanks, reversing to - strand was wrong. Now it is corrected.
      Attached Files

      Comment

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