Changes between Version 1 and Version 2 of SOPs/ShortReadExpDesign


Ignore:
Timestamp:
10/12/17 10:31:05 (7 years ago)
Author:
gbell
Comment:

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  • SOPs/ShortReadExpDesign

    v1 v2  
    88   * Longer and/or paired reads are surely beneficial if the experimental goal is
    99       * novel gene discovery: longer reads are much better at identifying novel splice junctions
     10   * According to [https://www.ncbi.nlm.nih.gov/pubmed/26100517 Chhangawala et al., 2015], 50-bp reads are adequate for identifying differentially expressed genes.  Identifying novel splice junctions, however, can benefit from paired and longer reads.
    1011   * For variant discovery, coverage is key, whether it's fewer long reads or more shorter reads (as long as the reads are long enough to map uniquely)
    1112 * How much read length is used for primers, adapters, barcodes, etc.?  Of course make sure that enough actual experimental DNA is left for effective mapping.
     13
    1214
    1315== If you are able to sequence more than one lane, how should the samples be partitioned? ==