Changes between Version 69 and Version 70 of SOPs/mapping


Ignore:
Timestamp:
09/21/20 16:00:08 (5 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/mapping

    v69 v70  
    22== Mapping short reads ==
    33
    4 
    5 
    6 === Regular mappers ===
    7 === [#splice_mappers Go to splice-aware mappers] ===
    8 
    9 Some choices for regular short-read mappers are
    10   * [#bwa BWA]
    11   * [#bowtie2 bowtie2]
    12   * [#bowtie bowtie]
    13 
     4'''Contents:'''
     5  * [#regular Regular mappers]
     6    * [#bwa BWA]
     7    * [#bowtie2 bowtie2]
     8    * [#bowtie bowtie]
     9  * [#splice_mappers Splice-aware mappers]
     10    * [#STAR STAR]
     11    * [#tophat2 Tophat 2]
     12    * [#tophat Tophat]
     13    * ''[#others others]''
     14
     15=== [=#regular Regular mappers] ===
    1416
    1517These mapping tools are useful for reads of DNA origin that should map to a continuous stretch of genomic DNA.  Some of these tools can tolerate short indels but they're not designed for reads that span a splice junction
    … …  
    110112These mappers permit the beginning and end of a read to map to (originate from) different places in the genome, which is common for spliced RNA.
    111113
    112 Some choices for regular short-read mappers are
    113   * [#STAR STAR]
    114   * [#tophat2 tophat2]
    115   * [#tophat tophat]
     114Some choices for regular short-read mappers are [#STAR STAR], [#tophat2 Tophat 2], and [#tophat Tophat].
    116115
    117116=== [=#STAR STAR] ===
    … …  
    258257  * '''--solexa1.3-quals''' or '''--phred64-quals'''     (for input quality scores from Illumina versions 1.3-1.7)
    259258
    260 == Others ==
     259== [=#others Others] ==
    261260
    262261  * [[https://daehwankimlab.github.io/hisat2/ | HISAT2]]: successor of TopHat2/HISAT