Question: TopHat Align Summary - whats a good results
gravatar for mbt
11 weeks ago by
mbt0 wrote:


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).


rna-seq tophat mapping hisat2 • 148 views
ADD COMMENTlink modified 11 weeks ago by Jennifer Hillman Jackson25k • written 11 weeks ago by mbt0
gravatar for Jennifer Hillman Jackson
11 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


Your goal is to maximize not only the number of reads that map but those pairs that map concordantly. These results show significant problems.

I would suggest double checking that you mapped against the intended target database/genome. Even with lower quality data, or data that needs some QA, higher mapping rates would be expected.

Tophat is an older tool and considered deprecated. Using newer tools methods is strongly recommended (example, use HISAT2 instead of Tophat). Please see the Galaxy RNA-seq Tutorials for example usage:

To troubleshoot/avoid common input problems, the Support FAQs here will help:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 11 weeks ago by Jennifer Hillman Jackson25k
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