Welcome to the help pages for the CRUK-CI Genomics Core. These pages will provide a good deal of information for users of the sequencing service.

As always, if you have any questions not found in this documentation [[genomics-helpdesk@cruk.cam.ac.uk|please email the Genomics help desk]].

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====== Contents ======

  * Submissions
    * [[submission:process|The Submission Process]]
    * [[submission:forms|Submission Forms]]
    * [[submission:slx_submissions|Sequencing Only (SLX) Submissions]]
    * [[submission:ont_submissions|Oxford Nanopore Sequencing Only Submissions]]
    * [[submission:ont_submissions_lps|Oxford Nanopore Library Prep (LPS) Submissions]]
    * [[submission:lps_submissions|Bulk DNA and RNA Library Prep (LPS) Submissions]]
    * [[submission:10x_submissions|10x Single Cell Submissions]]
    * [[submission:10x_visium|10x Visium Submissions (Spatial Transcriptomics)]]
    * [[submission:10x_xenium|10x Xenium Submissions (Spatial Transcriptomics)]]
    * [[submission:Single-cell FAQ|Single-cell FAQ]]
  * More Help for Submissions
    * [[submission:customprimers|Custom Primers for Sequencing]]
    * [[submission:indexkits|Index Kits and Barcodes]]
    * [[data:sharing|Sharing Data]]
    * [[submission::colourbalance|Illumina Barcoding Colour Balance]]
    * [[submission:barcodesearch|Index Kits and Barcodes Search Tool]]
    * Collaborator Specific Help
      * [[submission::collaborators:functionalgenomicscentre|Functional Genomics Centre]]
      * [[submission:direct_submissions|Direct Sequencing Submissions]]
  * After Sequencing - Dealing With Your Data
    * [[data:retrieval|Retrieving Sequencing Data]]
    * [[data:illumina|Illumina Sequencing]]
      * [[data:fastq|FASTQ Files and Index Reads]]
      * [[data:olink|Olink Sequencing Counts]]
    * [[data:ont|Oxford Nanopore Sequencing]]
    * [[data:xenium|10x Xenium Imaging]]
  * Help with Data after Sequencing
    * [[support:demultiplexing|Dealing with Demultiplexing Problems]]