Question: EstimateLibraryComplexity alternative for single-end sequencing?
gravatar for asta.tranholm
6 months ago by
asta.tranholm0 wrote:


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?

ADD COMMENTlink modified 6 months ago by RamRS30k • written 6 months ago by asta.tranholm0

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

ADD REPLYlink written 6 months ago by RamRS30k

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 might be of interest.

ADD REPLYlink written 6 months ago by ATpoint40k
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