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