Question: Re: Ngs Mapping Using Lastz
0
Thomas Jenner Pulikotial Augustine • 10 wrote:
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
ADD COMMENT
• link
•
modified 7.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
7.3 years ago by
Thomas Jenner Pulikotial Augustine • 10
