The result files included in the bundle-results folder available for download include:
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UMI_extracted .fastq files (If UMIs are included in the library prep)
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Trimmed .fastq files with fastqc (.html) and stats reports
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Aligned .bam files with alignment report
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Collapsed aligned .bam files and stats reports (if UMIs are included in the library prep)
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Coverage .bw files
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Gene counting .tsv files
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Normalized counts .tsv files
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are:
Raw and trimmed multi QC reports
Aligned log files
UMI_collapsed statistics
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 condition pairwise comparison (when differential gene expression is specified)
Multiqc reports (.html), plots (png) and tables (.txt)rseqc report
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.