Computational protocol: Novel modes of RNA editing in mitochondria

Similar protocols

Protocol publication

[…] A genomic paired-end library was constructed from total DNA and sequenced with Illumina MiSeq. Details on libraries are compiled in Supplementary Table S2. Cutadapt version 1.2.1 (http://journal.embnet.org/index.php/embnetjournal/article/view/200) was employed for adapter clipping, quality trimming and elimination of reads shorter than 20 nt. Reads were assembled with the Celera software runCA version 8.3rc2 (http://sourceforge.net/projects/wgs-assembler/ ()) using default parameters. Contigs originating from the mitochondrial genome were identified by sequence identity with previously determined mitochondrial chromosomes and modules (GenBank acc. nos. EU123536-8 and HQ28819-33) using BLAST at a hit-reporting threshold of 99% and then clustered with CD-HIT version 4.6 () employing the option -c 0.9. […]

Pipeline specifications

Software tools cutadapt, CD-HIT
Application WGS analysis
Chemicals Adenosine, Amino Acids, Cytosine, Inosine, Nucleotides, Uridine