Question: Tumor Purity and miRNA / small RNA pipeline
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gravatar for Chris_AI
10 weeks ago by
Chris_AI20
Chris_AI20 wrote:

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

ADD COMMENTlink modified 10 weeks ago by igor4.7k • written 10 weeks ago by Chris_AI20
1

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.

ADD REPLYlink written 10 weeks ago by Buffo550

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.

ADD REPLYlink written 10 weeks ago by Chris_AI20
0
gravatar for igor
10 weeks ago by
igor4.7k
United States
igor4.7k wrote:

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

For tumor clonality:

ADD COMMENTlink written 10 weeks ago by igor4.7k
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