Clarifying the meaning of Bowtie2's default alignment mode (noob question)
The default alignment mode of bowtie2 is "search for multiple alignments, report the best one".
As far as I understand this means that secondary and supplementary alignments will not be reported. Which means that
samtools view -f2304 sample_bowtie2Mapped.bam | wc -l
will always yield zero.
1) Is that correct?
2) How can multiple alignments be fetched nevertheless?
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Istvan Albert
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Aspire
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Aspire
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Have the flags explained
samtools flags 2304
0x900 2304 SECONDARY,SUPPLEMENTARY
then -f means:
-f INT only include reads with all of the FLAGs in INT present [0]
can an alignment be both secondary and supplementary at the same time? These are mutually exclusive terms.
If you wanted to include only the non-primary alignments and that you would need to do it in two steps.
First select the secondary, then the supplementary.
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