Hello,
For counting the read number and the mean coverage on the reference genome
using an Illumina read bam file (usually paired-end), would someone kindly
answer the following questions about Samtools view option difference between
"-F 4 -q 1" and "-F 4" after bwa mapping?
IF I USE: samtools view -b -h -F 4 -q 1 -S ${outputdir}/out.sam
>${outputdir}/uni_mapped.bam,
WILL THE MAPPING RESULT BE: Only the reads that each has a single best location
will be mapped (or counted)? I mean, if the read has two or more mapped
locations of the same mapping quality score, the read will NOT be counted.
Therefore this reads survived from this "-F 4 -q 1" can be called "uniquely
mapped reads".
IF I USE: "samtools view -b -h -F 4" without "-q 1" ,
THE MAPPING RESULTS:
1) If a read has multiple matching locations with different quality scores but
one of the locations is of the best mapping quality, will the read be mapped to
that best location, and not to other locations?
2) If a read has two or more matching locations with the equal quality score,
will the read be assigned to one of the locations RANDOMLY? Will that read have
more chance to be mapped to chromosome 1 and less chance to chromosome 2?
3) If I have 1 single read in the input bam file and if the read has matches to
10 locations, will the number of mapped reads to the reference genome be still
1, not 10?
4) If a reference genome is composed by 10 tandem repeats (no any other
sequences) and if the input read bam file has only one read and happened to be
one perfectly matched repeat, will the mean coverage of the entire reference
genome is 0.1 fold? Will the coverage depth of the actually covered portion is
one fold?
Best regards,
Xiu-Qing
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