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Old 05-07-2013, 08:11 AM   #1
mruizm
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Default how is the minimum read counts to do a transcriptome assembly?

Hi everyone, i have Illumina short read data of 2X150 bp tight now, araound of 12,35 G of data.
I want to know if you have knowledge about the exactly number of reads to do a good transcriptome assembly of a plant.
Best regards to everyone!
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Old 05-07-2013, 08:21 AM   #2
JackieBadger
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Depends on the ploidy of your organism and if you are aligning to a reference or not.
For de-novo bi-allelic SNP detection I have previously used a min of 20x and a min allele frequency of 20%.

I think with RADseq de-novo in a diploid organism around 30x is recommended per SNP.

If you have a reference to validate SNPs against you could probably go a little lower
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Old 05-07-2013, 11:03 AM   #3
mruizm
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Hi JackieBadger, the problem on my analysis is that i don't know about the ploidy of the organism and i'm not alignin to any reference because is a denovo transcriptome...
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Old 05-07-2013, 11:31 AM   #4
mruizm
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The only information that i know is that de genome of the plant is from the large of 325 Mb.
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