Hi,
I am new to Tophat and I have an alignment rate query.
I am trying to map RNASeq paired reads (100bp) to a reference genome using Tophat (v2.0.6) and I am returning an alignment rate of 26%. The –solexa-quals option improved the alignment rate slightly, altering other options from the default settings had no affect. I have 34,000 reads and I was expecting a higher rate.
tophat -p 2 --solexa-quals --b2-very-sensitive Homo_sapiens.GRCh37.67.cDNA_ncRNA UC07i.qfiltered.Bhg19.1.fq UC07i.qfiltered.Bhg19.2.fq
I used the same reads in Bowtie version 2.0.2 and returned an alignment rate of 90.5%
bowtie2 -p2 -x Homo_sapiens.GRCh37.67.cDNA_ncRNA -1 UC07i.qfiltered.Bhg19.1.fq -2 UC07i.qfiltered.Bhg19.2.fq -S UC07i.sam --very-sensitive-local
I understand that Bowtie2 is not appropriate for mapping RNASeq reads as it does not account for RNA splicing and Tophat uses end-to-end alignment.
Is it possible to improve the alignment rate for Tophat or can I assume that 26% is an appropriate rate?
The adapter sequences have been removed so I don't think trimming would be useful.
Thanks in advance!
I am new to Tophat and I have an alignment rate query.
I am trying to map RNASeq paired reads (100bp) to a reference genome using Tophat (v2.0.6) and I am returning an alignment rate of 26%. The –solexa-quals option improved the alignment rate slightly, altering other options from the default settings had no affect. I have 34,000 reads and I was expecting a higher rate.
tophat -p 2 --solexa-quals --b2-very-sensitive Homo_sapiens.GRCh37.67.cDNA_ncRNA UC07i.qfiltered.Bhg19.1.fq UC07i.qfiltered.Bhg19.2.fq
I used the same reads in Bowtie version 2.0.2 and returned an alignment rate of 90.5%
bowtie2 -p2 -x Homo_sapiens.GRCh37.67.cDNA_ncRNA -1 UC07i.qfiltered.Bhg19.1.fq -2 UC07i.qfiltered.Bhg19.2.fq -S UC07i.sam --very-sensitive-local
I understand that Bowtie2 is not appropriate for mapping RNASeq reads as it does not account for RNA splicing and Tophat uses end-to-end alignment.
Is it possible to improve the alignment rate for Tophat or can I assume that 26% is an appropriate rate?
The adapter sequences have been removed so I don't think trimming would be useful.
Thanks in advance!
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