reference sequence - splice sites

[marada]

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

[steven]

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.

[marada]

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.