Hi, <div><br></div><div>I&#39;m trying to map a data set containing 454 reads to a reference genome using LASTZ alignment package in Galaxy. I&#39;m following a workflow used for Illumina reads with the only change in the alignment package, i&#39;m using LASTZ instead of bowtie/bwa. The following is the procedure please correct me if it&#39;s wrong and do suggest any additional procedure to make the workflow better. </div>
<div><br></div><div>In addition to this i&#39;m, trying to do metagenomics analysis as well by following the procedure given in one of the video tutorials. I&#39;ve submitted the files for alignment and its been a day since the submission and the process has not yet started, could you tell me what could be the reason. The file size is 110Mb, under history the package indicate  &quot;Job is waiting run&quot;  how long does it usually take to initiate the process in the queue. Your suggestion&#39;s are valuable, thanks for developing Galaxy. </div>
<div><br></div><div>Kindly help, thank you. </div><div><br></div><div>1.Uploaded a FASTA file as input </div><div>2.Align using LASTZ </div><div>3.Filtering SAM files on bit-wise flag values </div><div>4.Finding how many reads are mapped to each chromosome </div>
<div>5.Sort the read counts </div><div>6.convert sam to bam </div><div>7.perform flagstat operation </div><div><br></div><div>Br, </div><div>Thomas </div>