Question: miRNA seq, problems with alignment
0
gravatar for adrian.ramirezdearellano
8 days ago by

Hi everyone. I'm having troubles analyzing some miRNA seq files.

First I used cutadapt to trim the universal adaptors. I confirmed that all adaptors and polyA were correctly trimmed by using fastqc. However, when i make the alignment versus my Homo Sapiens index the result is barely 12% (Which I think is very low).

I took the results of the alignment (around 300 IDs) and analyzed to obtain the differentially expressed miRNAs (around only 16)

I'm not an expert in the Field. I need help to increase the percentage of alignment and therefore the differentially expressed miRNAs.

Is there any suggestion to analyze it better?

rna-seq alignment • 49 views
ADD COMMENTlink written 8 days ago by adrian.ramirezdearellano0
1

Which aligner are you using for this? What is the length of the trimmed reads you are trying to align? Provide command line options used if you can. Try a miRNA specific pipeline if you are not using one.

ADD REPLYlink written 8 days ago by GenoMax96k

show us some examples of reads that didn't align

ADD REPLYlink written 8 days ago by Jeremy Leipzig19k
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