Find gene duplications in a draft genome assembly
Hi everyone, I have recently assembly a draft genome. I consider it has an acceptable quality based on the assessment I made and my biological goals. Before I have the genome assembly ready, I performed a de novo transcriptome assembly of this species and, after some analysis, I found some candidate genes to be duplicated in the genome. My idea to check this by mapping the reads to these transcripts (candidates) and to the genome and the check the positions of those reads that have mapped both. I am a beginner in this area, so I would like to know your ideas and advice about it.
I have both short and long reads but I think it would be better to use short ones in this case. So I would map reads to transcripts (candidates genes) with bowtie2, then filter the mapped reads and, then, map them to the genome. After that, I will need to find primary and secondary alignments of each read (if exists) and compare the transcripts to these regions. I have not thought about param settings but I have lost the pairing information after the first map of reads to candidate genes (only one read of the pair map). I need to make some tests to define the params.
Thanks in advance
I have both short and long reads but I think it would be better to use short ones in this case. So I would map reads to transcripts (candidates genes) with bowtie2, then filter the mapped reads and, then, map them to the genome. After that, I will need to find primary and secondary alignments of each read (if exists) and compare the transcripts to these regions. I have not thought about param settings but I have lost the pairing information after the first map of reads to candidate genes (only one read of the pair map). I need to make some tests to define the params.
Thanks in advance