IGV Bundle for Rhizophagus irregularis DAOM-197198

<p>Use these files to build&nbsp;your own genome browser for the &quot;Rhiir3&quot;&nbsp;<em>Rhizophagus&nbsp;irregularis</em> DAOM-197198 chromosome-scale genome assembly (PRJNA885267). Tracks available:</p> <p><strong>Gene annotation, based on Illumina and Nanopore RNA-Seq reads. </strong><br> Gene models were&nbsp;curated by excluding&nbsp;genes with InterPro domains related to&nbsp;transposable elements.<br> File: Rhiir3_PRJNA885267_genes.gff3</p> <p><strong>Repeat annotation. </strong><br> The repeat library was made using EDTA (Ou et al., 2019), and&nbsp;curated by excluding consensus sequences with InterPro domains of&nbsp;known cellular&nbsp;genes. Repeats were then masked using RepeatMasker&nbsp;(parameters&nbsp;-s -no_is -norna -nolow -div 40)&nbsp;(Smit et al., 2015).&nbsp;Unclassified repeats are grey-coloured and repeats classified into transposable elements categories are&nbsp;colour-coded: LINEs are blue, DNA transposons are pink and LTRs are green.<br> File: Rhiir3_PRJNA885267_repeats.gff3</p> <p><strong>Highly methylated CG sites,&nbsp;called via direct Nanopore genomic DNA sequencing of&nbsp;<em>R. irregularis </em>spores.<em>&nbsp;</em></strong><br> 161Gb of raw FAST5 files obtained from three R9.4.1 Nanopore flow cells were basecalled with Guppy5, producing 985,449 reads which were successfully processed by tombo&nbsp;(Stoiber et al., 2017)&nbsp;and used by DeepSignal2&nbsp;(Ni et al., 2019)&nbsp;to extract CG motifs and to call 5mC modifications using a human model (model.dp2.CG.R9.4_1D.human_hx1.bn17_sn16.both_bilstm.b17_s16_epoch4.ckpt.&nbsp;Only CG sites with &gt;80% 5mC are shown, and the track indicates&nbsp;methylation ratios measured as a fraction of 1 (0.80 to 1.00).<br> File: Rhiir3_PRJNA885267_high_meth_CG.bed</p> <p><strong>Index for CG methylation sites.</strong><br> File: Rhiir3_PRJNA885267_high_meth_CG.bed.idx</p> <p><strong>Nanopore RNA-Sequencing reads,&nbsp;poly(A)+ cDNA-PCR, from&nbsp;<em>R. irregularis</em> spores. </strong><br> Reads were trimmed of adapters and cleaned with seqclean to remove&nbsp;a&nbsp;percentage of undetermined bases,&nbsp;polyA tails,&nbsp;overall low complexity sequences and&nbsp;short terminal matches. Cleaned sequences were then mapped using minimap2 (options: -G&nbsp;max intron length=3000,&nbsp;-ax,&nbsp;map-ont).<br> File: Rhiir3_PRJNA885267_nano_cDNA.bam</p> <p><strong>Index for Nanopore RNA-Sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_nano_cDNA.bam.bai</p> <p><strong>Small RNA loci.</strong><br> 70,956,710 small RNA-Seq reads from two replicates of oxidised and two replicates of column-purified spore RNA&nbsp;(Dallaire et al., 2021) were used to run ShortStack&nbsp;(Axtell, 2013)&nbsp;(parameters --dicermin 20 --dicermax 27 --foldsize 300 --pad 200 --mincov 10.0rpm --strand_cutoff 0.8 --mmap r).<br> File: Rhiir3_PRJNA885267_small_RNA_loci.gff3</p> <p><strong>Small RNA sequencing reads.</strong><br> Shortstack small RNA-Seq&nbsp;alignments,&nbsp;with multi-mappers randomly distributed.<br> File: Rhiir3_PRJNA885267_small_RNA.bam<br> <br> <strong>Index for small RNA sequencing reads.</strong><br> File: Rhiir3_PRJNA885267_small_RNA.bam.bai</p>