Confused...

[DrDTonge]

Dear all,

I've run the SOLiD small RNA workflow (35bp reads) and have just downloaded my reads from the server following primary analysis (it was a barcoded run).

My confusion is that my average read length is 35bp from the csfasta file. I wasn't aware that the primary analysis removed the adapter sequences but this must be the case??

Best wishes,

Dan

[mbblack]

That's always been my experience with the *.csfasta and *.qual files I get. These contain the color space calls for each ligation, but none of the adapter sequence, other than its final base. You should get reads like (for a 50bp read):

>2_91_1302_F3
T23302110303101123023020203111121111210002110002110

with all but the terminal "T" of the adapter stripped out.

[DrDTonge]

Much appreciated.

D