Hello everyone,
I'm fairly new to bioinformatics as I've only recently started training. My PI gives me papers and asks me to follow their methods so I would learn. Currently, I'm learning hybrid de novo/reference guided assembly. Before getting into assembly and alignment, I have to pre-process the raw reads.
The authors say they assessed the quality of the data using fastqc, which I get. My problem is that they say they trimmed the first and last few bases of the reads that didn't map to the reference genome using prinseq. How could they do that? Prinseq doesn't seem to have this feature.
I tried using prinseq- and other trimming software- with guessed parameters but when I get to the assembly part, velvet produces empty files. I'm guessing that's because of my poor pre-processing.
I would really appreciate it if you could help me understand the method mentioned in the paper.
I'm fairly new to bioinformatics as I've only recently started training. My PI gives me papers and asks me to follow their methods so I would learn. Currently, I'm learning hybrid de novo/reference guided assembly. Before getting into assembly and alignment, I have to pre-process the raw reads.
The authors say they assessed the quality of the data using fastqc, which I get. My problem is that they say they trimmed the first and last few bases of the reads that didn't map to the reference genome using prinseq. How could they do that? Prinseq doesn't seem to have this feature.
I tried using prinseq- and other trimming software- with guessed parameters but when I get to the assembly part, velvet produces empty files. I'm guessing that's because of my poor pre-processing.
I would really appreciate it if you could help me understand the method mentioned in the paper.
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