question about Clip adapter in FASTX-toolkit for small RNA

Question

[rob.costa1234]

I am clipping the adapter from a FASTq file. There are three options in Galaxy version of FASTX-toolkit-

Output only clipped sequences (i.e. sequences which contained the adapter) Output only non-cliped sequence (i.e Sequence which did not contain the adapter) Output both clipped and non-clipped sequences

when I see the instructions @ http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html I could not figure out which one may be most appropriate.

I want to get the FASTq fiel after cliping adapter. To get read which dont have adapter sequence in initial FASTq file as well as reads where ad adapter reads are clipped. Any pointer which out put option should be the right one. I tried 1st and 3rd option both are different and dont have adapter seq.

Thanks

Answer 1

[Shyam]

For smallRNA seq, you need to go with the reads with adapter clipped only. Any reads without the adapters are probably not the smallRNA because they are shorter than the read size (18 - 25nt) and read size is usually 50nt. The reads without any adapter sequences in them are most probably the degraded longer RNA.

Answer 2

[igor]

The point of the clipper tool is to clip adapter sequences. You can choose if you want reads that were not clipped (adapter not found) and/or reads that were clipped (adapter found). If you want to keep the adapter sequence, then do not run the clipper tool.

[rob.costa1234]

What will be the general rule to take reads only from where adapter has been clipped and discard rest of reads which dont have adapter seq to begin with. I am interested in small RNA seq and want to remove true seq small RNA illlumina adapter seq. In publications I dont find any consensus.

[igor]

Then output only clipped sequence.