small rnaseq data quality question - before using mirdeep2
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6.7 years ago
Mamta ▴ 500

HI all,

I have small rna data generated on Nextseq 500. Before using mirdeep2, I wanted to be assured of the quality of the data.

I used cutadapt on 1 sample- and this is what I see : Please let me know if I need to do anything (more processing, any concerns with data) before i can use mirdeep on it.

what was done: Using cutadapt removed adapter sequence and shorter than 15nt reads.

What I see: 1. Per base quality drops after position 36 (score 14) 2. Good peak around 22-23 but also smaller peak at 75 (Iam assuming this is where the adapter removal failed? Should I remove this?) 3. Kmer content has a peak at position 47-50 and 62-68 - should i be concerned? 4. Overrepresented sequence has no hit (top one is 6%) Should I look into it?

Anyone with experimnce with small rnaseq and mirdeep please advice! Thanks in advance! Mamta

mir-seq small Rna seq fastqc mirdeep • 1.5k views

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