Changes between Version 7 and Version 8 of SOPs/mapping

Timestamp:

09/11/13 16:46:32 (12 years ago)

Author:

byuan

Comment:

--

SOPs/mapping

@@ -20 +20 @@
   * '''-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
-  * '''--solexa1.3-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]]
+  * '''--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)
@@ -37 +38 @@
   * '''-L <int>'''     length of seed substrings; must be >3 and <32 (default=22)
   * '''-N <int>'''     max # mismatches in seed alignment; can be 0 or 1 (default=0)
-  * '''--phred64'''    (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]]
+  * '''--phred64'''    (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]]
   * '''-S'''           name of SAM output file
 
@@ -68 +69 @@
 The parameters included in the sample command are:
   * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
-  * '''--phred64-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]]
+  * '''--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]]
+  * '''--phred64-quals''' or '''solexa1.3-quals'''   (if input quals are from GA Pipeline ver. >= 1.3 before Illumina 1.8)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]