Computational protocol: Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

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Protocol publication

[…] The sequencing fastq files were converted to fasta format and reads without Ns were retained for further analysis. The evaluation of quality scores was conducted as in the FastQC suite. The 3' adapter and HD signatures (4 assigned nt at the 3’ and 5’ end of the insert []) were trimmed using perfect string matching on the first 7 nucleotides of the adapter (TGGAATT). Next, the files were converted from redundant to non-redundant format and the results were summarised into redundant and non-redundant size class distributions [].In non-redundant format, the reads were mapped to the reference genome (D. melanogaster v 6.11) and associated annotations, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [,]. The reads were also mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21 []. The sRNA analysis was conducted using the UEA sRNA Workbench, custom-made Perl and R scripts. The presence plots were created in R, v 3.4.0. […]

Pipeline specifications

Software tools FastQC, PatMaN
Databases miRBase
Application Nucleotide sequence alignment
Organisms Drosophila melanogaster