Hi,
Can anyone show me a recommended command line input to achieve this? I have never used the program before and am afraid of entering inappropriate values for one of the many paramters.
Or is there a good reference dealing with the run settings for this application?
Thanks in advance,
Aligners will generally use two files for paired ends and the order is considered important.
The default is probably fine.
And yes, for paired reads, you will run the aligner twice, once with the read 1 fastq, and once with read 2 fastq. You use the sampe command to make a .sam file that takes as input both alignment files. It will assume that the first read from one alignment file matches the first read in the other file, and so on, so it will set the flags and the insert size appropriately in the .sam output.
So don't quality-filter individual reads out of the fastq's, because they need to stay in paired order between the two files.
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The default, or if the quality is poor at tail: "aln -q15".