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Old 08-12-2014, 12:07 PM   #1
sckinta
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Location: United States

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Question Depth of RNAseq with sensitive detection

Hi,

I am going to do RNAseq on multiple conditions with 3 replicates for each, to de novo assembly the transcriptome and identify some low expressed factors (<1% in transcriptome) in different conditions. Quantitative comparison is required, and detection of isoform changes even SNPs are preferred.

Hiseq with 76 or 100bp PE reads is obviously the first choice. Since we have 12 conditions, plus 3 replicates, 36 samples will be sequenced in total. If a depth of 100-200 M reads per sample is recommended for sensitive detection, it means we need at least 9 lanes for all my samples. That will be a huge expense.

I am wondering whether it is possible to reduce depth to 40-50 M reads per samples, considering I have 3 replicates. Or what kind of design (depth, replicate arrangement in lanes ...) can be an alternative plan with least compromise on my purpose but lowest price?

BTW, the genome size is estimated as 1300 Mb.

Thank you

Last edited by sckinta; 08-12-2014 at 12:22 PM.
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