i have a very simple question which may not be very simple,
i have extracted some reads from a bam file, and have made a denovo assembly using
soapdenovo. then i
blast these contigs against my reference genome. i got some hits. but the reads belong to different positions in the bam file. so i know the position of the hit in the reference genome but i also want to know the position in the bam file. but soapdenovo does not keep track of the reads in the assembly.
if i could get the information that during assembly, which read went to which contig that would solve my problem.
i was wondering if there is another assembler that keep tracks of the reads in the assembly would be great or any other indirect solution.