Hello,
I am having trouble getting some of my software to work to match a long complex insertion and deletion of the serotonin transporter gene (SLC6A4) promoter region (EMBL/GenBank accession No. X76753). We have WGS using hg19 as the reference. There are as many as 16 variants of this area in some racial ethnic groups.
Can somebody tell me how to find the exact position of this promoter region so that I can inspect my BAM files with IGV? There is a well-known SNP (RS25531) that is close by that I can visualize with no problem (ch17:28,564,346), but I cannot visualize this promoter.
I have drawn a blank with my more experienced colleagues here.
Thanks in advance for any help.
JY
0 answers
No answers yet.
Log in to answer this question.
It's not really clear what you're trying to do.
What WGS data are you working with? How long are the reads? Are you looking for a long insertion/deletion in the WGS dataset(s)?
If that's the case, then it seems as if you might have to do a de novo assembly rather than mapping onto a reference.
If the promoter of your gene has not been experimentally determined, just use the TSS +/- 1kb as a general rough guide.