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Re^2: Deconvolutinng FastQ files

by Anonymous Monk
on Aug 07, 2012 at 13:37 UTC ( #985986=note: print w/replies, xml ) Need Help??

in reply to Re: Deconvolutinng FastQ files
in thread Deconvolutinng FastQ files

Thank you frozenjoy. With FastQ on galaxy I need to trim the first three letters for my record to be able use the barcode splitting function. I haven't tried the stand-alone version yet. I will give that a go once I can get it to work on my computer. These three letters are important for my analysis, so I am not entirely sure if I can use FastX's barcode splitter tool. I am playing around with the galaxy version of it at present.

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Re^3: Deconvolutinng FastQ files
by frozenwithjoy (Priest) on Aug 07, 2012 at 15:35 UTC
    I took a look at and I think I've figured out a solution. I haven't tested it, but if you change line 161 from:
    unless $barcode =~ m/^[AGCT]+$/;
    unless $barcode =~ m/^[AGCTN]+$/;
    then you should be able to prefix your barcodes w/ 3 N's as long as you set --mismatches to at least 3 on the command line when running the script.

    One caveat is that you will want to toss out any reads that have any Ns in the first X bases (where X = 3+ barcode length). Have you run FastQC? If so, this will tell you the per base N content. It probably won't be an issue if you've already done preliminary filtering based on Illumina's Y/N flags (assuming Illumina sequencing, of course).

    Also, (depending on your computer, of course) I suspect will run a lot faster at the CLI than on Galaxy (at least if you are using the public galaxy server).

    Edit: to avoid the potential problem w/ Ns, just use some other non-nucleotide character!

      Thank you frozenwithjoy. I should give this a go too. We are thinking about running our own Galaxy server in the EC2, so the revised fastx_barcode_splitter might come in handy. Browseruk's script below works super fast, I am not sure how might compare.

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