The result files included in the bundle-results folder available for download are:
Trimmed_statistics Raw and trimmed _fastqc reportmulti QC reports
Aligned log files
UMI_collapsed statistics
Gene counting .tsv file for each sample
Counting_summary folderCounting_summary folder with three different output .tsv files
o « Summary_sum »: This file contains all the reads mapped to the genome including multimappers
o « Summary_average » :This file is similar to the « summary_sum » but the number of reads is divided by the number of time these reads are aligned to the genome.
o « Summary_unique »: This file contains only the uniquely mapped reads to the genome and is typically used as input for DESeq 2 analysis.
Transcript_concentration folder (Only for CORALL data analysis, obtained with Mix2 )
For Differential expression analysis: normalized counts .tsv files, pairwise summary .txt and results .tsv files for each pairwise comparison (when differential gene expression is specified)
Multiqc rseqc report
NOTE: Trimmed.fastq files, aligned.bam and , collapsed.bam files and gene counting files for each sample are not part of the bundle-result folder but can be downloaded separately. Please be mindful that depending on the size and number of files to download, you may need to purchase additional quotas.
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