Question: smallRNA seq mapping issue
gravatar for khzina
19 months ago by
khzina0 wrote:

I am quite new to NGS data analysis, I want to map small RNA seq to reference genome. I used SRA small RNA seq samples, particularly miRNA seq to miRbase genome index and piRNA to piRbase genome index. but I could not find a mapping results more than 5% for any samples even for already published SRA samples. I want to ask what method should I use or what mistake I could be doing.

I used normal bowtie mapping command

bowtie2 -x miRbase or piRBase index -U SRR3303398.fastaq -S output.sam
rna-seq • 391 views
ADD COMMENTlink modified 19 months ago by WouterDeCoster44k • written 19 months ago by khzina0

In the SRA entry it says RNA-seq of Merkel cells. Are you sure this is smallRNA-seq? In "normal" RNA-seq the small RNA species are typically not well captured during RNA isolation and subsequent library prep which could explain your results.

ADD REPLYlink written 19 months ago by ATpoint36k

I used the search term small RNA seq, and got these results and selected this SRA file from them. How can i make sure its small RNA seq and when i get it what should i do . can you elaborate some steps

ADD REPLYlink written 18 months ago by khzina0
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