I will very soon have results from MiSeq and need to analyze them, in particular do the alignment. The samples have been prepared with a directional RNA-seq protocol, single end. Read length is up to ~300 bp. This is on homo sapiens.
I have a couple of very basic questions. Background: Usually I start my analysis from aligned sequences coming from HiSeq, I have no experience whatsoever with MiSeq. I am the "computer guy", and am not interacting with the instrument itself.
Thanks!
I have a couple of very basic questions. Background: Usually I start my analysis from aligned sequences coming from HiSeq, I have no experience whatsoever with MiSeq. I am the "computer guy", and am not interacting with the instrument itself.
- How does the output format of MiSeq look like? Is it FASTA or FASTQ or something else?
- (main question) What is the best software for alignment? Can I use BWA? Do I need to perform putative PCR duplicate removal first, or removal of ribosomal sequences? Or can I just BWA the output and that's it? Anything else I need to be aware of, especially with respect to MiSeq?
- The Illumina website alludes to something called "MiSeq Reporter" and states that it can do sequencing as well - is it worth pursuing?
Thanks!
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