Hi,
I'm trying to map a data set containing 454 reads to a reference genome using LASTZ alignment package in Galaxy. I'm following a workflow used for Illumina reads with the only change in the alignment package, i'm using LASTZ instead of bowtie/bwa. The following is the procedure please correct me if it's wrong and do suggest any additional procedure to make the workflow better.
In addition to this i'm, trying to do metagenomics analysis as well by following the procedure given in one of the video tutorials. I'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 "Job is waiting run" how long does it usually take to initiate the process in the queue. Your suggestion's are valuable, thanks for developing Galaxy.
Kindly help, thank you.
1.Uploaded a FASTA file as input 2.Align using LASTZ 3.Filtering SAM files on bit-wise flag values 4.Finding how many reads are mapped to each chromosome 5.Sort the read counts 6.convert sam to bam 7.perform flagstat operation
Br, Thomas