hi all!
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.
It has been a while since I worked with this, but I think these are the read IDs velvet is using internally.
In the output folder there should be a file called "Sequences". It is basically a fasta file with the input reads. The fasta header should look like this:
It starts with the original read ID followed by the vlevets internals read ID (6 in this case). I do not know at the moment what the last number means.
it was really helpful. actually there was no description of the "Sequences" file in the manual.
thanks alot