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It wasn't recognizing the -i because it was a long "-" not a short one. Must have been from copying from word into the command line. WOW!
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This is a pretty common problem on both PC/mac OS. You should turn off "smart" hyphens (and other smart things) in keyboard preferences. -
Nice work j.cappellazzi!
I hadn't heard of that hyphen issue - bit of a trap!
The "./" in my command refers to a 'relative' path. I.e., it will look for a folder that is in your current directory. This is in contrast to absolute paths, i.e., "/home/qiime/Desktop/Hilo_New/" that will work no matter where you run them from.
I think the problem with my original command is that the folder name and the name in the command were slightly different. You created a folder called "FastX-filterFastq", but the command is trying to create output here "./fastX-filterFastq/". Note the lower-case 'f' in fastX.
Anyway, glad you got it working!
Cheers,
Matt.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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