[Genome] Download first intron sequences

[Brooke Rhead]

Hello Celina,

One of our engineers has highlighted characteristics of the output from 
the Table Browser that you can use to distinguish intron number:

=====
Embedded in the very long name assigned to each intron is a sequence number:

NM_016749_intron_5_0_chr1_136014281_f
                  ^

The number just after "intron" is the sequence number which starts at
0 *for the lowest coordinates*, so she also needs to consider strand,
which is the last character -- 'f' for forward, 'r' for reverse.  If
the strand is r then she should use the intron with the highest
sequence number instead to get the first intron in the transcript.

The other numbers in the name after the intron number are the padding 
amount, the chrom, the 1-based start coordinate in case the item names 
are not unique, then the strand.
=====

I hope this helps you get the information you need.  Please let us know 
if you have any further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Montemayor, Celina wrote:
> Hi, I was wondering if I could get some advice regarding how to
> download the coordinates of the frist introns of my list of genes (I
> need a BED file)? I used the table browser to paste my gene IDs and
> download intron sequences; the output I obtained looks like this:
> 
> chr1	 136014280	 136014811
> NM_016749_intron_5_0_chr1_136014281_f
> 
> Is there a way for me discriminate which are the coordinates
> corresponding to the first introns?
> 
> Thanks for your help,
> 
> Celina Montemayor, MD  Graduate Student, Pereira lab Baylor College of
> Medicine _______________________________________________ Genome
> maillist  -  Genome at soe.ucsc.edu 
> http://www.soe.ucsc.edu/mailman/listinfo/genome