Question: TopHat Align Summary - whats a good results
0
mbt • 0 wrote:
Howdy,
Just got the results back from top hap - looked at align summary
Not sure how to read it
Left reads:
Input : 25951385
Mapped : 231015 ( 0.9% of input)
of these: 114189 (49.4%) have multiple alignments (8625 have >20)
Right reads:
Input : 25951385
Mapped : 233499 ( 0.9% of input)
of these: 111823 (47.9%) have multiple alignments (8625 have >20)
0.9% overall read mapping rate.
Aligned pairs: 124107
of these: 85304 (68.7%) have multiple alignments
2055 ( 1.7%) are discordant alignments
0.5% concordant pair alignment rate.
Is this a good. Is this result typical or has the alignment failed. It says only 0.9% mapping rate ( I presume thats a good thing given that only very small proportion of genome is coding).
Mike
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modified 11 weeks ago
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Jennifer Hillman Jackson ♦ 25k
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written
11 weeks ago by
mbt • 0
