Supplementary Data - Nanopore cDNA With and Without mtDNA

<p>Update (v1.5.8-SUPcaller): added scripts and data files for mt-Nd1 comparisons for different basecaller versions:</p> <ul> <li>LAST_gci_*.csv - gap-compressed identity statistics</li> <li>compStats_*.csv - called base-level statistics</li> <li>process.txt - script example file demonstrating how to generate statistics</li> <li>smealgol.r - R script to generate gap-compressed identities from LAST output</li> <li>est_vs_actual.png - density plots comparing gap-compressed identity with mean estimated accuracy from the caller</li> <li>GCI_albacore_guppy.png - violin plots comparing gap-compressed identity with different callers</li> <li>BaseQ_vs_GCI.png - scatter plots comparing gap-compressed identity with mean estimated accuracy from the caller</li> </ul> <p>Update (v1.5.7-Nd1Reads): added mt-Nd1 read subset from CGDec2017 run:</p> <ul> <li>4T1-WT_reads_CGDec2017_singlePlusMulti.tar</li> </ul> <p>Update (v1.5.6-countAnalysis): added / updated a script to convert transcript mappings to a count table:</p> <ul> <li>count_analysis.r</li> </ul> <p>Update (v1.5.5-Int): added intermediate (post-demultiplexing) demonstration dataset:</p> <ul> <li>SampleDESet_60k_demultiplexed.tar.gz</li> </ul> <p>Also updated count tables and DESeq2 results:</p> <ul> <li>raw_counts_2019-Nov-29.csv</li> <li>DE_orig_VST_GRCm38_CG_GL261_2019-Nov-29.csv.gz</li> <li>DE_shrunk_VST_GRCm38_CG_GL261_2019-Nov-29.csv.gz</li> </ul> <p>Update (v1.5.4-MT): updated demonstration dataset (now 40Mb) to include mitochondrial transcripts, and exclude non-target sequences from chimeric reads:</p> <ul> <li>reads_SampleDESet_sampled_60k.fastq.gz</li> <li>Mm_subset.GRCm38.ensembl_v98.fa</li> </ul> <p>Update (v1.5.3-Ensembl): added/updated Ensembl reference transcripts, including non-coding RNA:</p> <ul> <li>ensembl_mm10_geneFeatureLocations.txt.gz - genome annotation</li> <li>Mus_musculus.GRCm38.ensembl_v98.fa.gz - transcript sequences</li> </ul> <p>Update (v1.5.2-Demo): added 60Mb demonstration dataset for teaching / learning purposes (<em>reads_SampleDESet_sampled_60k.fastq.gz</em>). This dataset can be used for testing demultiplexing, or carrying out differential expression analysis on nanopore reads. There are 15k reads sampled from each run (subset on ~300 genes), plus 7.5k chimeric reads from the Dec17 run, plus 7.5k reads sampled from from CG009/BC08. The gene subset includes ~100 genes differentially-expressed between 4T1WT and 4T1&rho;⁰ cell lines, plus an additional ~200 genes with minimal differential expression observed between any 4T1 cell lines (i.e. a housekeeping gene set):</p> <ul> <li>BC01, BC02, BC04, BC06 - 4T1 cell line reads from three sequencing runs (005, 005, 004, Dec17)</li> <li>BC03, BC05, BC07 - 4T1&rho;⁰ (without mtDNA) cell line reads from three sequencing runs (005, 004, Dec17)</li> <li>BC08 - 4T1&rho;⁰SC (from subcutaneous tumour) cell line reads from one sequencing run (009)</li> </ul> <p>[note: v1.5.1-Demo has the wrong sequence ID for BC08 reads]</p> <p>Update (v1.5.0-Called): added full 4T1 call set (called using guppy high-accuracy v3.2.2), gene transcript count tables, and differential expression results</p> <p>Update (v1.4.1-Chimeric): added more example called chimeric reads of various [unclassified] categories</p> <p>Update (v1.4.0-Chimeric): added example chimeric reads, one formed [presumably] during sample prep [&quot;conjugation&quot;], another formed in-silico [&quot;double read&quot;]</p> <p>Update (v1.3.0-DESeq2): added count table and metadata file for DESeq2 analysis</p> <p>Update (v1.2.1-10k): added 10k of FASTQ reads from a more recent run (part of the same differential expression project).</p> <p>Supplementary data to go with David Eccles&#39; poster about nanopore cDNA sequencing with and without mitochondrial DNA.</p> <p>Reference mouse mtDNA and mtDNA reads from 4T1 cells (from MinION cDNA sequencing, and from SRA run SRR6747859).</p> <ul> <li>fwd_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-forward orientation</li> <li>rev_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-reverse orientation</li> <li>fwd_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1&rho;0 strain (no mitochondrial DNA), filtered as transcript-forward orientation</li> <li>rev_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1&rho;0 strain (no mitochondrial DNA), filtered as transcript-reverse orientation</li> </ul> <p>Other intermediate data files are also included, see `4way_mapping_process.txt` for more details.</p> <p>The mpileup differential coverage script can be found <a href="https://github.com/gringer/bioinfscripts/blob/master/mpileupDC.pl">here</a>.</p>