Question: How to find which genes are missing?
0
gravatar for guardsquirrel
8 weeks ago by
guardsquirrel0 wrote:

Hi everyone, I've made an assembly for a chloroplast genome, however I'm confused as to what I have to do next...

I'm trying to identify any genes that are normally present in chloroplasts but are missing in my assembly. How could I go about doing this?

I've already identified my plant based on phylogenies focusing on rbcL genes and rps4+rps4-trnS intergenic spacer. I have the fasta of the assembly and I've seen people using bedtools but I don't know which commands to use (if I use bowtie2 to make a .sam output, wouldn't that just use my non-assembled sequences? since I used getorganelle to assemble my genome and all I have from that is the fasta.

Thank you so much.

ADD COMMENTlink modified 4 weeks ago by Rashedul Islam340 • written 8 weeks ago by guardsquirrel0
1
gravatar for Rashedul Islam
4 weeks ago by
Canada
Rashedul Islam340 wrote:

If I understand you question correctly - you want to get the genes that are not present in known chloroplasts genomes and you have the assembled genes of the chloroplast genome of your interest.

For that you can use blastn.

ADD COMMENTlink written 4 weeks ago by Rashedul Islam340
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