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Old 07-26-2011, 12:11 AM   #1
DrDTonge
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Default SOLiD Barcoded Adapter Trimming

Dear all,

I've run a barcoded SOLiD run with a set of 12 small RNA samples. Following the sequencing run, I've performed the primary analysis and downloaded the csfasta (F35) and qual files.

On visualising the reads, they are all 35nt as expected and I therefore need to remove adapter sequence. My question is what sequence I should be expecting...

As I understand, the barcode is read in a separate sequencing reaction and therefore is not part of this 35 read. Also as the read is read from P1, it is not the P2 adapter as this is more than 35 away from the sequence start site.

My only guess is that it is the barcode "adapter" which seems to be PCR'd in when using the various barcoded primers.

Can anyone confirm whether I am correct? And if so, have the sequence of this adapter (I presume it is conservered across all the barcodes)...

My working tell me the sequencing should be...

CGCCTTGGCCGTACAGCAG

however this doesn't give a good % trim (around 20 %)

Many thanks,

D
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Old 07-26-2011, 12:31 AM   #2
DrDTonge
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or the reverse complement

CTGCTGTACGGCCAAGGCG
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Old 07-26-2011, 07:43 AM   #3
westerman
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Are you doing your trimming in base-space or color-space?
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Old 07-26-2011, 11:43 PM   #4
DrDTonge
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I'm doing it in colour-space using CLC Bio...
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Old 12-06-2011, 07:33 AM   #5
vini
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Hi DrDTonge,

I have a similar SOLiD data of small RNA samples with every read being 35bp long. Did you find a solution to problem you posted? Is "CGCCTTGGCCGTACAGCAG" the only adapter that you trimmed?

Thanks
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