Hi All,
The job at hand it to align 17 million 50 bp illumina reads onto a reference scaffold through Seqman Ngen. The results from the alignment show that approx. 16 million reads remain unaligned when ran with default parameters. Even tweaking the parameters (minmatch percentage=80 and match size=17) improved the alignment but only by a few percentage points.
Alignment done with same samples with Newbler showed 97% reads mapping onto the reference.
I dont have a license for Newbler and I am trying to make Seqman Ngen work. Any suggestions to improve the assembly.
Thanks,
The job at hand it to align 17 million 50 bp illumina reads onto a reference scaffold through Seqman Ngen. The results from the alignment show that approx. 16 million reads remain unaligned when ran with default parameters. Even tweaking the parameters (minmatch percentage=80 and match size=17) improved the alignment but only by a few percentage points.
Alignment done with same samples with Newbler showed 97% reads mapping onto the reference.
I dont have a license for Newbler and I am trying to make Seqman Ngen work. Any suggestions to improve the assembly.
Thanks,
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