Changes between Version 39 and Version 40 of SOPs/mapping


Ignore:
Timestamp:
03/13/17 12:23:51 (8 years ago)
Author:
thiruvil
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/mapping

    v39 v40  
    5858  * '''--best'''                 (in the case of multi-mapped reads, keep only the best hit(s))   
    5959  * '''--sam'''                  to get SAM output format (which is the best format for downstream analysis)
     60  * '''--all'''                  report all alignments (much slower, ie. turn-off -k option)
     61
    6062Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
    6163  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)