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=== 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 }}} |
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