Question: rnaseq sequence analysis and trimming
gravatar for Björn
3.1 years ago by
Björn40 wrote:

Hi, I received sequences from RNAseq for mirna from a company. I have following questions regarding the sequences. As company provided following sequencing kit was used

eg. of sequnce

Overrepresented sequences

Sequence                                                                 Count        Percentage                       Possible Source
                                                                                  2733553     24.346957954015203         No Hit
GGCTGGTCCGATGGTAGTGGGTTATCAGAACT  1389076     12.372094108631375          No Hit
TCCTGTACTGAGCTGCCCCGA                             498271         4.437954225400096          No Hit
  1. What is the difference between "adapter" and "index" sequences ? How to trim those sequences using trimmomatic or cutadapt ? The index sequences are different in different samples. However, few sequences show no index sequences but it should be there ?

  2. What are the empty sequences shown in "over represented sequences" ? HOw to remove those ?

  3. How do I make sure that I remove necessary adapters, index sequences using cutadapt or trimmomatic. The sequence length is 37 or more bp and after removing those adapter and index the final sequence length was still more than 25 bp. For miRNA, the sequence length should be short if I am not wrong. So, I think I am doing something wrong

ADD COMMENTlink modified 3.1 years ago by WouterDeCoster43k • written 3.1 years ago by Björn40

Take a look at the Trimmomatic manual, chapter "ILLUMINACLIP":

ADD REPLYlink written 3.1 years ago by Macspider3.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1582 users visited in the last hour