miRNA pipeline guide

Question

[jiovy1991]

Hello, i'm an university student, as an end-of-course project I have to perform a pipeline for miRNA, as in the image ...., you could suggest me which tools to use and how to proceed. Thank you all

Answer 1

[giorgio.giurato]

Hi, You can use cutadapt to remove adapter sequences and bowtie to map the reads. A good tool Is sRNAbench or SPAR

[jiovy1991]

thanks for the answer, the problem is mainly related to the computational resources we have (a machine with 16gb ram and i7-7700HQ), in fact trying to index the entire human genome (hg38) with BWA (used in a tutorial in the classroom) crashes due to lack of resources ... I'll try the tools mentioned.

[giu.lat82]

Try to download the indexed genome from here http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html