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Old 02-19-2014, 07:47 AM   #1
Location: Berlin

Join Date: Jul 2013
Posts: 20
Default Is 30000 reads too low for mapping (miRNAs)

Hello community,
I have just received a fastq file of a study i am conducting.
It had an overall poor quality, and after filetering reads according to quality and size (minQV=17, min length=16), the number of reads decreased from 95428 to 29635. And the quality increase markedly.

My question is if it would be still possible to use those ~30000 readss fro mapping.

Best regards and thanks!
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Old 02-19-2014, 08:42 AM   #2
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Location: East Coast USA

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Posts: 7,080

You can use any number of reads to do the mapping. Whether you are going to get anything useful out of the mapping is the real question.

What species do you work with and what kind of analysis (counts/discovery) are you looking to do?
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Old 02-19-2014, 08:52 AM   #3
Location: Berlin

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Hi GenoMax,
thank you for the quick reply.
I work with cattle and I would like to do counts analysis.
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Old 02-19-2014, 10:18 AM   #4
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Location: San Diego, CA

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Even with just counting I generally wouldn't recommend less than 1M reads per sample. But I'm curious to hear about other people's guidelines for miRNA-seq
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