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- Do both R1 and R2 reads have separate alignment records?
- Does the SAM file contain both aligned and un-aligned reads?
- What is the order of the alignment records in this SAM file?
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- Do both R1 and R2 reads have separate alignment records?
- yes, they must, because there were 1,184,360 R1+R2 reads and an equal number of alignment records
- Does the SAM file contain both aligned and un-aligned reads?
- yes, it must, because there were 1,184,360 R1+R2 reads and an equal number of alignment records
- What is the order of the alignment records in this SAM file?
- the names occur in the exact same order as they did in the FASTQ, except that they come in pairs
- the R1 read comes first, then its corresponding R2
- this ordering is called read name ordering
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Using cut to isolate fields
Recall the format of a SAM/BAM file alignment record:
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Suppose you wanted to look only at field 3 (contig name) values in the SAM file. You can do this with the handy cut command. Below is a simple example where you're asking cut to display the 3rd of the last 10 alignments.
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