Hi, <br><br>I&#39;m a new user, learning how to use Galaxy while I wait for my 454 results. So I&#39;m not actually playing with any data yet but I&#39;m trying to set up a draft workflow as practice. Two issues:<br><br>Issue 1. <br>
<br>I am having trouble with the &#39;manipulate fastq&#39; command. Without this, my workflow saves quickly and seems fine, but when I include even a (seemingly simple) &#39;manipulate fastq&#39; step, it tries to save for many minutes, unsuccessfully, until I get sick of it and close the window. <br>
<br>Issue 2.<br><br>Well this isn&#39;t really an issue, just a request for advice! My dataset will be a barcoded amplicon library, containing 8 different gene regions (which I can recognise from the amplicon-specific primer sequences) amplified in 64 different individuals (which I can recognise by an individual-specific barcode sequence). I thought I&#39;d set up a workflow with the following steps: 1) convert to FASTQ format. 2) grooming, filtering to remove short reads etc. 3) &#39;manipulate FASTQ&#39; to match all sequences containing one of the eight reverse primer sequences, and reverse-complement them. 4) FASTQ--tabular format conversion. 5) eight separate &#39;select&#39; steps to select sequences with a match to either the forward primer or the reverse-complemented reverse primer of the desired gene region. <br>
<br>My question is: does this seem sensible? Is there a more efficient way to do this that I haven&#39;t discovered yet? I was thinking I&#39;d then set up another workflow to label barcoded individuals, for I could use each of the eight gene &#39;output files&#39; in turn as input. <br>
<br><br>Thanks so much for this service! The screencasts are especially great. <br><br>Pip Griffin<br>University of Melbourne, Australia<br>