Changes between Version 8 and Version 9 of SOPs/mapping

Timestamp:

09/12/13 09:35:53 (11 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -16 +16 @@
 }}}
 
-The parameters included in the sample command are:
+Parameters included in the sample command:
   * '''-l/--seedlen <int>'''     seed length for -n (default: 28) -- Set to longest possible length of high-quality bases.  Use the FastQC output to determine length of high-quality positions.
   * '''-n/--seedmms <int>'''     max mismatches in seed (can be 0-3, default: -n 2)
   * '''-k <int>'''               report up to <int> good alignments per read (default: 1) -- If you want only uniquely mapped reads, however, also use '-m 1' to ignore multi-mapped reads
-  * '''--solexa-quals'''         (if input quals are from GA Pipeline ver. < 1.3)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]
-  * '''--solexa1.3-quals''' or '''--phred64-quals'''     (if input quals are from GA Pipeline ver. >= 1.3 and before Illumina 1.8)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]
   * '''--best'''                 (in the case of multi-mapped reads, keep only the best hit(s))   
   * '''--sam'''                  to get SAM output format (which is the best format for downstream analysis)
+Choices 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.
+  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)
+  * '''--solexa1.3-quals''' or '''--phred64-quals'''     (for input quality scores from Illumina versions 1.3-1.7)
+  * '''--phred33-quals'''         (default "Sanger format"; for input quality scores from Illumina versions 1.8 and later)
 
 To see other parameters log into tak and type '''bowtie'''