Question: miRNA seq, problems with alignment
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

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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