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Old 05-09-2016, 10:25 PM   #1
aurorasea1
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Default HISeq Read Depth

I am new in learning how to do bioinformatics, and I have been handed over a set of HISEq data files to analyse differential expression.
Sorry if this is a really simple question, but is there a way to find out the sequencing depth?

Thank you very much
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Old 05-10-2016, 12:45 AM   #2
dpryan
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Default

Align the sequence, count the number of alignments, multiply that by the average read length and divide by the genome size.

Having said that, "coverage" isn't normally used in RNAseq because it's not very meaningful. What matters is the read number, percentage of alignments and the final counts you get.
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