Hey @all
I am new to NGS, just in bevore...
I have mapped a mammalian genome to a reference genome (~2,4GB) with BWA and all worked very well, so far. Now I am really unsure how to continue.
When I now want to work with my mapped genome and I want detect genes in this genome, I am not sure if it is better to just search the gene on the reference genome to identify the scaffold, and then assemble the subset of reads that mapped to that scaffold to get the final gene sequend of "my" mapped gene, or should I assemble the whole genome, and then start my work.
How should i care for SNPregions? shoud I do the so called phasing or does the assembler do all the work?!?
Many Thanks in advance!!!!!
I am new to NGS, just in bevore...
I have mapped a mammalian genome to a reference genome (~2,4GB) with BWA and all worked very well, so far. Now I am really unsure how to continue.
When I now want to work with my mapped genome and I want detect genes in this genome, I am not sure if it is better to just search the gene on the reference genome to identify the scaffold, and then assemble the subset of reads that mapped to that scaffold to get the final gene sequend of "my" mapped gene, or should I assemble the whole genome, and then start my work.
How should i care for SNPregions? shoud I do the so called phasing or does the assembler do all the work?!?
Many Thanks in advance!!!!!
