What output files do I get for QuantSeq and LUTHOR HD data analysis with Kangooroo?

The result files included in the bundle-results folder available for download are:

• Raw, trimmed and aligned multi QC reports.

• Trimmed stats and aligned log files.

• UMI_collapsing statistics (Not for QuantSeq FWD library prep without UMIs).

• Gene_counting_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.

• For Differential expression analysis: normalized counts .tsv files, pairwise summary .tsv and results .tsv files for each pairwise comparison (when differential gene expression is specified).

• PCA summary and plot.

• PDF report summarizing all the results.

NOTE: Trimmed.fastq files, aligned.bam, 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.

If additional quotas are required, please contact sales@lexogen.com.