Since I couldn’t find one readily available anywhere online, I wrote a small PERL script to split a FASTQ file into two files: a FASTA and a QUAL file. Click above to view more.
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So, I’ve ben working on my thesis, and I determined that using Cairo Graphics + GWT was really ineffecient, and way too much work. This is largely in part due to my discovery of the Google Chart Tools and, more specifically, the Google Visualization API. Both do pretty much the same thing, they create neat-looking graphs with very little demands on the user. The difference between the two is that Chart Tools create 2D images that you can stick on your website, rendered in less than a second. The Visualization API creates interactive graphs, which is, for me, 50 times better.
FASTA files with sequences from next-generation sequencing projects can be large and are usually stored as compressed files using compression algorithms such as GZIP or ZIP. If you do not want to extract all the data or create another copy of the file when performing a BLAST search, you can combine the file extraction and the BLAST search using a pipe in Unix-based operating systems and tell the BLAST program to use the standard input. Here is one example on how to do that (assuming you have a GZIP compressed FASTA file): Continue reading
The following two subroutines can be used as a drop in replacement for Math::NumberCruncher. This is useful when trying to limit the number of dependencies of your perl script. Continue reading