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degradome data adapter removal

I am processing some of the publicly available degradome data from 4 different projects. in two projects I found the adapter sequence to be used for analysis. but in other two, 3′-adapter random primer was used.

So how to identify and remove the 3' random adapter from the data before processing. Give me insight in relation to degradome data analysis.

degradome fastqc adapter
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written by 1000-Logan • 1000-Logan

I've never analysed Degrome data before, but I'm pretty sure random 3' adaptors aren't possible. Are you sure its not the reverse RT primer that is ranodm, or that the 3' adaptor contians a stretch of random nucleotides within a constant backbone? Adaptors need constant sequences so that they can be subjected to PCR, and have landing pads for sequencing primers, bridge amplification etc.

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written by i.sudbery i.sudbery

I am not sure, but I have run FastQC and matched the reads with other primers databases as well. It doesn't match with any primer. Although I have retained 22 nucleotides irrespective of adapter sequences for furhter analysis. Can you suggest if I am goin in the right direction or not

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written by 1000-Logan • 1000-Logan

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