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any solution to multiple alignment rate in eukaryotes

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

rna-seq tophat2 bowtie2
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updated by Ram Ram • written by zizigolu zizigolu

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

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written by 5heikki 5heikki

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.

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written by Devon Ryan Devon Ryan

thank you both

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written by zizigolu zizigolu

1 answer

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

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updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

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