Hi,
I am using dwgsim from the dnaa package to simulate short read pairs from a reference genome.
What I eventually want to do is assess different aligners on the basis of the reads that align to the right position.
1.
I was looking at the documentation on http://sourceforge.net/apps/mediawik...ome_Simulation
and I'm trying to understand what my readname means, it is:
Chr1_1514706_1515213_1:1:0_1:0:0_0/1
So,
Chr1 = contig name
1514213 = start position 1 (from the mutated reference?)
1515213 = start position 2
and then I don't get the rest..?
2.
Are reads in _1.fq 5' reads and those in _2.fq 3' reads?
3.
What does this line in the output mean?
chr1 745 A R +
OR
chr1 15454 - A +
OR
chr1 87846 T C -
4.
My quality scores are all '1'?
5.
I would like to remove all errors caused by the actual sequencer/technology completely. Would that mean I need to make -e and -E = 0?
Cheers!~
I am using dwgsim from the dnaa package to simulate short read pairs from a reference genome.
What I eventually want to do is assess different aligners on the basis of the reads that align to the right position.
1.
I was looking at the documentation on http://sourceforge.net/apps/mediawik...ome_Simulation
and I'm trying to understand what my readname means, it is:
Chr1_1514706_1515213_1:1:0_1:0:0_0/1
So,
Chr1 = contig name
1514213 = start position 1 (from the mutated reference?)
1515213 = start position 2
and then I don't get the rest..?
2.
Are reads in _1.fq 5' reads and those in _2.fq 3' reads?
3.
What does this line in the output mean?
chr1 745 A R +
OR
chr1 15454 - A +
OR
chr1 87846 T C -
4.
My quality scores are all '1'?
5.
I would like to remove all errors caused by the actual sequencer/technology completely. Would that mean I need to make -e and -E = 0?
Cheers!~
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