== 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 included in 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 included in 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'''.

'''Other tools'''

Many other regular mapping tools are also available, although they generally require a tool-specific indexed version of the genome.

== Splice-aware mappers ==

These mappers permit the beginning and end of a read to map to (originate from) different places in the genome, which is common for spliced RNA.

'''[http://tophat.cbcb.umd.edu/ tophat version 1]'''

Running TopHat version 1 requires a change to a user's environment on tak (and only applies to the specific tak session.  First run this command: 
{{{
export PATH="/usr/local/share/tophat1:$PATH"
}}}
and then check that your terminal will use the correct TopHat version:
{{{
tophat --version
}}}

Sample command:
{{{
bsub tophat -o s_7_tophat_out --phred64-quals --no-novel-juncs --segment-length 20 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
}}}

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]]