FASTQC is primarily designed to QC whole-genome shotgun sequencing data.

Should I trim adapters from my Illumina reads? This depends on the objective of your experiments. In case you are sequencing for counting applications like differential gene expression (DGE) RNA-seq analysis, ChIP-seq, ATAC-seq, read trimming is generally not required anymore when using modern aligners.  For such studies local aligners or pseudo-aligners should be used. Modern "local aligners" like STAR, BWA-MEM, HISAT2, will "soft-clip" non-matching sequences.

By default, we will generate Tag-Seq and Batch-Tag-Seq gene expression profiling data that incorporate Unique Molecular Identifiers (UMIs) in the sequence reads. (This FAQ provides information on the usage of UMIs:  https://dnatech.genomecenter.ucdavis.edu/faqs/should-i-remove-pcr-duplicates-from-my-rna-seq-data/ ). Please note that the UMIs provide optional additional data analysis options; for many applications, the UMI information

Should I remove PCR duplicates from my RNA-seq data? The short and generalized answer to the question "Should I remove PCR duplicates from my RNA-seq data?" is in most cases NO.  For some scenarios, de-duplification can be helpful, but only when using UMIs. Please see the details below. The vast majority of RNA-seq data are analyzed without duplicate removal. Duplicate removal is not possible for single-read data (without UMIs).

We will deliver the complete data set generated by the PacBio Sequel to you securely via Bioshare. For push-button type secondary analyses (combining data for up to 2 SMRT-cells e.g.

By default you will receive gzip compressed FASTQ data, as individual files  for each sample (demultiplexed).  The demultiplexing is included in the service if you provide us the barcodes sequences on the submission form. The files will be available for download from our secure SLIMS server. You will receive only the reads from clusters passing the Illumina quality filter, also called Illumina chastity filter  -

We deliver sequencing data via two portals: SLIMS for Illumina data, and BioShare for PacBio and Nanopore data. Both portals offer secure access to the data and support several download protocols.

Strand-Specific RNA-Seq Libraries RNA-Seq (conventional) after Poly-A enrichment or ribodepletion: By default we generate strand-specific RNA-seq libraries. Strand-specific (also known as stranded or directional) RNA-seq libraries substantially enhance the value of an RNA-seq experiment. They add information on the originating strand and thus can precisely delineate the boundaries of transcripts in regions with genes on opposite strands. There are several ways to accomplish strand-specificity.

Please note that when opening an Illumina sequence fastq file it is expected that the first few thousand reads are of comparatively low quality and frequently contain "N"s.  An "N" means that the Illumina software was not able to make a basecall for this base. The reads at the beginning and end of the sequence data files originate from the edges of the flowcells, where imaging is more difficult, thus these reads show below average quality.

We are using the PerkinElmer NEXTflex™ Small RNA-Seq kit for the generation of micro RNA and small RNA-seq libraries because it significantly reduces sequence-specific biases in the library preparation.  For this purpose the adapters oligonucleotides contain 4 randomized bases at the ligation junctions.  These randomized bases should be removed by trimming before mapping the sequence reads.