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Old 07-11-2011, 04:39 AM   #1
Location: MRC

Join Date: May 2011
Posts: 23
Default Small RNA - Reads too long after trimming

I have run a batch of small RNA samples on the SOLiD system. Following sequencing, I've trimmed the adapters (in colour space) using CLC Bio.

The statistics are as follows...

Reads Trimmed: 98.1%
Average Length after trim: 33.7bp

It is the latter figure that is worrying me...just wondering if anyone has experienced this? My expectation was a read average of ~22 and only 15,000reads fit this catergory.


DrDTonge is offline   Reply With Quote
Old 07-11-2011, 07:37 PM   #2
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Location: Sydney

Join Date: Feb 2011
Posts: 149

What was the total read count after adapter processing? What % of reads were ~22nt (15000 out of? ) ?

Depending on the library, we do get a distribution of sizes up to 30 nt, but most of it would be between 20 and 24nt long (i'd say usually between 90 and 95% of processed). I'm not sure about the Solid sRNA sample prep (we use illumina), but perhaps you might need to check if the library was prepared properly.

Also, we once had very low throughput but turned out that our adapter sequence was wrong (shorter than it should have been), so you might want to check this too.
Kennels is offline   Reply With Quote

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