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Old 09-23-2014, 02:54 AM   #5
Location: India

Join Date: Jun 2013
Posts: 14
Default Subsampling

Dear Brian Bushnell,
I did subsampling and after subsmapling N50 value is getting substantially increased.
I have 101300000 reads with expected mitochondrial genome size of 715000 base pairs.
But problem persists even after picking file with less contig numbers (around 90-100) with good N50 is that the alignment result with raw reads to its contig file is horrible (almost 91% failure).

Can anyone let me know further processing? Since genome is mitochondrial, I don't have much options also for multiple seq alignment with related fasta files.
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