any solution to multiple alignment rate in eukaryotes

Question

[zizigolu]

Sorry guys,

This is my tophat result

Reads:
          Input     :  16286258
           Mapped   :  15989053 (98.2% of input)
            of these:   7149891 (44.7%) have multiple alignments (51923 have >20)
98.2% overall read mapping rate.

I also tried with -D 20 -R 3 k 2 options but the rate of multiple alignment is the same, do you have please any suggestion in this regards?

Thank you

[5heikki]

Since Eukaryotes are in general at least diploid isn't multiple alignment rate expected?

[Devon Ryan]

Ploidy doesn't affect the rate of multimapping, since reference genomes are typically haploid. However, the nature of the underlying data will and no settings will change that.

[zizigolu]

thank you both

Answer 1

[Antonio R. Franco]

98.2% of mapped reads can be considered high. In my hands, I got lower than 92% with nice and good quality sequencing. Take a look at this link to see some other opinions. Users get 85-90% of mapped sequences when using tophat. The link provides with some extra statistical values you will find useful

This high percentage of mapped sequences use to lead to a high percentage of multimapped reads that makes your mapping less useful than expected, like is your case