Conversion From Sam To Bed With Max Information
I am trying to convert my sam file into bed file in such a way that i will keep some information from the sam file.
I am primarily interested in keeping the actual short sequences in the bed format so that i do not lose track.
I used sam to bam and then bedtools but i ended up getting something like this
chr1 123 456 0 255 +
I have so many short sequences and how will i know which of my sequence is which