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

• UMI_extracted .fastq files (If UMIs are included in the library prep)

• Trimmed .fastq files with fastqc (.html) and stats reports / Trimmed statistics and Trimmed_statistics and trimmed_fastqc report

• Aligned .bam files with alignment report / Aligned log files

• Collapsed aligned .bam files and stats reports (if UMIs are included in the library prep) / UMI_collapsed statisticsCoverage .bw files

• Gene counting .tsv filesfile for each samplessample

• Counting_summary folder

• Transcript_concentration .? folder (Only for CORALL data analysis)

• Counting_summary .tsv file

• DEG, obtained with Mix2 )

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

• Multiqc rseqc report

NOTE: Trimmed.fastq files, aligned.bam and alignedcollapsed.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 the files to download, you may need to purchase additional quotas for download. If this is the case

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

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