Dear UCSC Genome Browser staff,
I have positions of small sequence reads on human genome in BED format.
Example (first line of BED file)
Chr4 22428658 22428696 108
I want to intersect these genomic regions with introns of known genes. I
obtained the intronic regions of all genes on chromosome 4.
Example (first 2 lines of intronic regions as in BED format)
Chr4 22359681 22429441 uc003gqp.2_intron_3_0_chr4_22359682_f 0 +
Chr4 22429599 22429602 uc003gqp.2_intron_4_0_chr4_22429600_f 0 +
I used a tool from PSU called galaxy which simply intersects genomic regions
from both BED files. The results of the intersection is:
Chr4 22428658 22428696 108
In the intron regions file, I have coordinates of an intron but, do not have
which gene that intron belongs to and if that intronic region has repeat
regions.
How can I create a BED file that has intronic regions of chr4 and gene name and
repeat region as coloumn
example:
Chr4 22359681 22429441 uc003gqp.2_intron_3_0_chr4_22359682_f 0 + GeneX REpeat
regionxxx
How can this be done. I appreciate your help.
Thank you.
s
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