== Mapping short reads ==


== Regular mappers ==

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 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]'''

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"
}}}

The parameters used on the sample command are:
  * '''-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
  * '''--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]]
  * '''--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)

To see other parameters log into tak and type '''bowtie''' 


'''[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 ==