== Create a bowtie index ==

bowtie-build input.fasta output_index_name

== Working with samtools to summarize an alignment ==

If you have a sorted, indexed bam file:

{{{
samtools idxstats bamfile.bam
}}}

returns a 4 column format of reference feature, length, # of mapped reads, # of unmapped reads (in case of paired end?)

To summarize the total, you can use awk to add up the entries in the 3rd column:

{{{
samtools idxstats bamfile.bam | awk '{sum += $3}END{print sum}'
}}}


=== Map Quality ===

A value of 255 indicates that mapping quality is not available.

=== Tally multimapping reads within a  region ===
The XA tag should have information about alternate hits.
{{{
samtools view wt_tc_2.bam chrIV:160995-163154 | cut -f12 | sort | uniq -c
}}}