Alignment of mirna on specific organism data from mirbase

Question

[otieno43]

I have micro-RNA sequences that I need to align specifically to Drosophilar melanogaster mature microRNA from mirbase using bowtie. Have realized the fasta sequence of mature miRNA in mirbase contain all the organisms that whose microRNAs have been sequenced and submitted. I was wondering how I can extract/or specifically use D. melanogaster as reference as opposed to using all the mature miRNAs.

[Pierre Lindenbaum]

Review all your previous questions and validate or comment the answers (green tick on the left):

• How to obtain a data frame from "SeuratObject".
• Use of Scater for QC in scRNA-seq Analysis: How to remove cells with less than certain number of genes supported with certain number of reads
• Where and How to find TruSeq Universal Adapter file: TruSeq3-PE.fa
• Error in executing STAR Aligner

[Ram]

Do not type in a sentence to use as tags. Use relevant subject matter keywords. I'll try and fix it for you this time but please apply yourself a little more in the future.

Answer 1

[shelkmike]

A simple solution is to download the file https://mirbase.org/download/mature.fa , then open it in a text editor (for example, Notepad++) and manually copy all sequences that have "Drosophila melanogaster" in their titles to another file.

[Pierre Lindenbaum]

A simple solution (...) then open it in a text editor (for example, Notepad++) and manually copy all sequences that have "Drosophila melanogaster" in their titles to another file.

no, this is not a simple solution.

[shelkmike]

There are different definitions of simplicity.

[Ram]

Sure, simple as in easy and simple as in foolish (like in simpleton). Your solution is along the latter lines.

Answer 2

[Pierre Lindenbaum]

assuming https://mirbase.org/download/mature.fa there is only one line per sequence and there is 'Drosophila melanogaster' in each header:

wget -q -O - "https://mirbase.org/download/mature.fa" |\
grep -F 'Drosophila melanogaster' -A1 --no-group-separator > melanogaster.fa

[otieno43]

Thank you, sorted this out.

[Pierre Lindenbaum]

Please accept the answer so the question is marked solved on the website. To do that, click on the green check mark on the left side of the answer.