EstimateLibraryComplexity alternative for single-end sequencing?

Question

[asta.tranholm]

Hi,

I have an RNAseq dataset which was sequenced out with single-end settings. I would like to carry out the equivalent of the tool EstimateLibraryComplexity from the picard package, however, the tool is selectively used to paired-end data. I was wondering if anyone knows of a tool which works in a similar way but for single-end sequenced data?

[Ram]

Hi, on Biostars, you don't need a # with tags.

[ATpoint]

For RNA-seq duplicates are normal and expected. I would not bother with any tool tbh. Just align your data, check that you have a high percentage of reads mapping to exons and then proceed with downstream analysis. Additional QC via PCA might make sense. As an alternative to Picard, PreSeq http://smithlabresearch.org/software/preseq/ might be of interest.