Assembly of DNA from .bam file

Question

[Triple Nipple]

From a .bam file of RNA sequence reads that are aligned to a mouse reference genome, how can I get a new bam file that contains this same genome assembled in reference to mm10 reference genome. If I made things clear I need to get one long read sequence for each location and not many reads like it's the case with this .bam file.

For bases that in some reads (and not all) they seem to be mutated compared to reference, I need to have the most "probable" base, and in bases that aren't available, I also need them to be specified.

I would really appreciate your help and advice on doing this.

Thanks

Answer 1

[WouterDeCoster]

The term you are looking for is a consensus sequence. Take a look at this post: Generating consensus sequence from bam file
By chance, I also saw this today using Alfred for consensus.

Answer 2

[swbarnes2]

From a .bam file of RNA sequence reads that are aligned to a mouse reference genome, how can I get a new bam file that contains this same genome assembled in reference to mm10 reference genome.

It's probably simplest to just realign to the genome.

I need to get one long read sequence for each location

You are going to have gaps between genes and between introns. Wouldn't you be better off making a consensus from your transcriptome alignment? (For those RNA sequences where you have enough coverage)