Tumor Purity and miRNA / small RNA pipeline

Question

[ResearchR]

Dear all,

I would like to ask you for two suggestions:

1. If got an incredible amount of miRNA-Seq data. Can anybody of you recommend a pipline for quality-control and alignment?

2. I would like to compute the tumor purity from whole gnome seq tumor (with matching control) data. I know that it is hard to get the tumor purity in silico, but I would like to incorporate this information in an analysis pipline I am developing. I "googled" some tools, but I could not find any reports from users concerning the performance. Does anyone of you have a recommendation?

Thanks and best wishes,

Chris

[Buffo]

miRNA-seq data from small rna-seq library? If it is true, you can try Bowtie (v1) for alignment (recommended for short reads), for quality control try with fastqc, it works for me.

[ResearchR]

Yep, it is small rna-seq library. I thought about using RNA-SeQC for the QC step and STAR aligner (with proper parameters). As far as I know, STAR and Bowtie (v1) have quite similar performance, when it comes to short reads, despite the fact that STAR is way faster.

Answer 1

[igor]

You can check some previous posts for miRNA-seq processing:

• best STAR options for miRNA mapping?
• What is the most popular and best tools/pipeline for small RNA seq analysis?

For tumor clonality:

• Tumor clonality algorithms