How tos and FAQs

What data will I get after my sequencing experiment is finished?

You can receive data (results) in any format you wish. However, if you have no specific requirements, you will receive from us the following standard sequencing outputs:

 


Illumina technology

Data

  • Single-end sequencing – 1 individual FASTQ file for each sub-library (i.e. each index or index combination)
  • Paired-end sequencing – 2 individual FASTQ files (Mate1.fastq and Mate2.fastq) for each sub-library (i.e. each index or index combination)
  • Data will be de-multiplexed based on adaptor index combination and compressed in .gz format.

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • Sequencing report (basic statistics, chemistry used)
  • Raw data processing description
  • MultiQC report (html format)

 


PacBio technology

Data

  • Raw sequencing data of subreads in BAM format
  • Circular consensus reads (CCS) in BAM format
  • Data will be de-multiplexed according to assigned SMRT bell adaptor indexes, accompanied with index data file .pbi (e.g. demux.subreads.bam + demux.subreads.bam.pbi and demux.CCS.bam + demux.CCS.bam.pbi)

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • PacBio SMRT sequencing report including:
    • Productivity table
    • Polymerase reads table
    • Polymerase Reads with Full Passes table
    • All Subreads table
    • Demultiplexing table
    • CCS reads table
  • Raw data processing description

 


Oxford Nanopore technology

Data

  • Data in fast5 format (raw data) as follows:
    • fast5_fail - raw reads before basecalling, which did not pass quality control
    • fast5_pass - raw reads before basecalling, which passed quality control
    • fast5_skip - raw reads before basecalling, which the data analysis software was not able to process
  • Data in FASTQ format as follows:
    • fastq_fail - .fastq passing quality control
    • fastq_pass - .fastq not passing quality control

Reports

  • Sample QC report (passed/not passed, chemistry used and parameters measured)
  • Library QC report (passed/not passed, chemistry used and parameters measured)
  • Sequencing report (basic statistics, chemistry used)
  • Raw data processing description
  • Nanoplot QC report (html format)

 


Please notice that our bioinformaticians can provide any data output you may need including development of custom data analysis pipelines. For more information please contact us.

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