mpileup for rna-editing

[diya]

Hi,

I am trying to find RNA-Editing sites using mpileup.. I have 4 samples and when I run the command I have the following output. I am not sure as to how to interpret the results.. Any help on this is really appreciated..

chr1 155983024 t 0 * * 0 * * 0 * * 1 < H
chr1 155983032 t 0 * * 0 * * 0 * * 1 < H
chr1 155983047 t 0 * * 0 * * 0 * * 1 < H
chr1 155983102 t 0 * * 0 * * 0 * * 1 < H
chr1 155983134 t 0 * * 0 * * 0 * * 1 < H


Thanks,

[rnaseek]

mpileup output gives for each reference base location, the number of reads aligned, the read bases, and quality score for the read bases.

In the example given, the fourth sample has just one read and the remaining samples do not have any reads aligned at the reference bases.

Here is pileup homepage giving more details

http://samtools.sourceforge.net/pileup.shtml