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I have a fasta file with a thousand sequences with a distribution of lengths between 100 and 150bp. I would like to add Ns to all sequences whose length is <150. I know it is possible but thus far I have yet to find anything to easily do this. Please help. Thanks!
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Cross-posted:
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Not fast, but something like:
Code:perl -e 'while(<>) {if (/^>/) {print;next}; chomp; print $_,"N" x (150-length($_)),"\n"}' in.fastaComment
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That looks like it should be plenty fast enough, more likely to be limited by the read speed of the hard drive than the speed of the code.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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