Hi, just want to say that I'm a total newb so bear with me!
I have some bacterial WGS data from Ion Torrent system, and my lab has Geneious software which I'm using to do de novo assembly (among other things). I downloaded the new MIRA plugin for Geneious, and ran it with my reads but it quit on me because it detected very high coverage (>80x). Also the Geneious default assembler is taking muuuuch longer than usual to assemble it. I looked back at the data and this strain had a lot more reads than the other strains, so I've decided to throw out some of the reads.
I had trimmed the data already, but what I really need is for someone to tell me how to randomly select ~2 million reads to throw out! Can I just delete the first 2 million in the fastq file? For some reason I haven't been able to find any info on how to do this, kinda feel like it's a dumb question haha.
I have some bacterial WGS data from Ion Torrent system, and my lab has Geneious software which I'm using to do de novo assembly (among other things). I downloaded the new MIRA plugin for Geneious, and ran it with my reads but it quit on me because it detected very high coverage (>80x). Also the Geneious default assembler is taking muuuuch longer than usual to assemble it. I looked back at the data and this strain had a lot more reads than the other strains, so I've decided to throw out some of the reads.
I had trimmed the data already, but what I really need is for someone to tell me how to randomly select ~2 million reads to throw out! Can I just delete the first 2 million in the fastq file? For some reason I haven't been able to find any info on how to do this, kinda feel like it's a dumb question haha.
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