RNA-seq Data Analysis Protocol

Thirty libraries of paired-end short reads obtained with Illumina NextSeq550 sequencing platform were analyzed. Sequencing quality and length distributions were assessed using FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.5. Cutadapt software version 1.9.1 [38 ] was used to remove sequencing adapters, and Prinseq-lite software version 0.20.4 [39 (link)] was implemented for filtering with the following criteria: length not less than 100 bases, mean Phred quality score not less than 30. In case if one read in a pair did not meet the above criteria, the whole pair was discarded from analysis. Additionally, Prinseq option ‘-derep 1’ was employed in order to remove possible optical replicates.
Libraries of short reads were aligned to the reference genome version SolTub_3.0 taken from Ensembl plants database [29 (link)] using STAR aligner version 2.5.3a [40 (link)].

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Kochetov A.V., Egorova A.A., Glagoleva A.Y., Strygina K.V., Khlestkina E.K., Gerasimova S.V., Shatskaya N.V., Vasilyev G.V., Afonnikov D.A., Shmakov N.A., Antonova O.Y., Alpatyeva N.V., Khiutti A., Afanasenko O.S, & Gavrilenko T.A. (2020). The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes. BMC Plant Biology, 20(Suppl 1), 350.

Publication 2020

NextSeq550 sequencing platform

Genome Plants Possible

Corresponding Organization : Siberian Branch of the Russian Academy of Sciences

Other organizations : N.I. Vavilov Research Institute of Plant Industry, All-Russian Institute of Plant Protection

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Variable analysis

independent variables

Sequencing platform (Illumina NextSeq550)
Sequencing quality and length distribution assessment using FastQC
Adapter removal using Cutadapt
Filtering using Prinseq-lite with criteria: length not less than 100 bases, mean Phred quality score not less than 30, and removal of optical replicates

dependent variables

Quality and length of sequencing reads

control variables

Reference genome version SolTub_3.0 from Ensembl plants database
STAR aligner version 2.5.3a for read alignment

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