Bed file score , mismatch , and other column information

Question

[Whoknows]

Hi

I created a sam via Bowtie my bowtie index was plant mature miRNA and precursor and my query was smallRNA, then i made bed file of sam with BEDOPS.

My question is, how should I specify the number of mismatch?

And second, what is excatly score column?

thanks

Answer 1

[Dan D]

Hi pcsam.2008,

The BED spec doesn't have a provision for specifying mismatches. The format is orginally intended for visualizing mapped reads on a genome browser. The score column is an arbitrary value, intended to specify the grayscale intensity (0 = pure white, 1000 = solid black) for display of a given read. You could use this to provide a qualitative representation of the number of mismatches (or just base it on the alignment score).

Other formats, like CIGAR (which is present for each mapped read in a BAM file), will specify the exact number of mismatches.