What output files do I get with Kangooroo?

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

• Trimmed_statistics and trimmed_fastqc report

• Aligned log files

• UMI_collapsed statistics

• Gene counting .tsv file for each sample

• 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.

• 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 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.