Using the defaults and then testing the resulting SAM output seems to be what most folks are doing if they do not have access to the original library construction methods (e.g. size selection). Both SAM Tools and Picard are in Galaxy. This is a useful post where the options are discussed:

Is the data Illumina? The data source may be able to tell you if the adapter sequence was actually sequenced and/or if it was removed already or not. If present or you just suspect it is present, they would also have access to the Illumina fasta adapter data. You could also test with FastQC (before or after alignment, maybe on just a sample), then perform a clip based on those results, and re-run. See the tools in 'NGS: QC and manipulation' to perform these tasks.

Going forward, please send questions as a new thread directly to our mailing list at galaxy-u...@bx.psu.edu.


Galaxy team

On 7/10/12 5:36 AM, asma.bioi...@gmail.com wrote:
Does anyone got correct answer, how to extract the correct distance between two 

One naive question, how can I find the adapter sequence length?


Jennifer Jackson

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