Mapping microRNA reads to Genome and non-coding RNAs

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9.4 years ago

Zammy ▴ 20

Hello everyone

I hope I am posting in the right section. I am sure this question has been asked several times before and I have been going through discussion on similar topics on Biostars but I am still confused and hoping I could get a more simple answer based on my beginner level in NGS data analysis.

I am trying to perform miRNA-seq analysis. I Have ten samples. I performed adapter removal and trimming of reads using FastX toolkit. Now I have reads ranging from 17 to 44 nucleotides. I then used these file as input for bowtie and mapped my samples to hg19. I now have SAM file for each sample.

What I want to do next is :

Distribution/composition analysis of reads according to their size. i.e how many reads are of length 20,21,22 and so on. So I could make a bar plot or graph.
To find out which and how many reads in my samples map to GenBank entries and rFam database (rRNA, scRNA, snoRNA, snRNA and tRNA).

Regards

Zammy

microrna small-RNA-sequencing next-gen • 2.6k views

ADD COMMENT • link updated 2.1 years ago by Ram 43k • written 9.4 years ago by Zammy ▴ 20

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What I am looking to do is something like this:

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ADD REPLY • link updated 2.1 years ago by Ram 43k • written 9.4 years ago by Zammy ▴ 20

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Hey, do you mind sharing any information you got so far about your questions!..any leads to solve the problem? Thanks

ADD REPLY • link updated 2.1 years ago by Ram 43k • written 9.0 years ago by justinfanyi • 0

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