Changes between Version 4 and Version 5 of SOPs/mapping

Timestamp:

06/12/13 09:43:57 (12 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -7 +7 @@
 These 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
 
-One may choose between bowtie version 1 (faster but ignores indels) and bowtie version 2 (slower but allows indels).  For a feature comparision, see [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml How is Bowtie 2 different from Bowtie 1?]
+One may choose between bowtie version 1 (faster but ignores indels) and bowtie version 2 (slower but performs gapped alignment (i.e., indels)).  For a feature comparision, see [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml How is Bowtie 2 different from Bowtie 1?]
 
 '''[http://bowtie-bio.sourceforge.net/index.shtml bowtie version 1]'''
@@ -13 +13 @@
 Sample command:
 {{{
-bsub "bowtie  -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt ../s7_mm9.k1.n2.l36.best.sam"
+bsub "bowtie  -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt s7_mm9.k1.n2.l36.best.sam"
 }}}
 
@@ -29 +29 @@
 '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie version 2]'''
 
+Sample command:
+{{{
+bsub "bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt -S s7_mm9.L22.N1.sam"
+}}}
+
+The parameters used on the sample command are:
+  * '''-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]]
+  * '''-S'''           name of SAM output file
+
+bowtie2 can also perform local alignments where the unaligned end(s) of a read are clipped (so, for example, remaining adapter won't prevent alignment) by adding the argument '''--local'''.
+
+
+
 == Splice-aware mappers ==