Changes between Version 40 and Version 41 of SOPs/mapping

Timestamp:

03/13/17 12:26:28 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/mapping

@@ -55 +55 @@
   * '''-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
+  * '''-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; use --all to report all alignments (much slower, ie. turn-off -k option)
   * '''--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)
-  * '''--all'''                  report all alignments (much slower, ie. turn-off -k option)
 
 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.