We are currently trying to analyse Solid RNA-seq data using tophat and/or bowtie.
With default settings tophat is able to align about 35% of reads, whereas bowtie on default is able to align 53%!!
I'm assuming that tophat first runs bowtie then tried to align reads that span exon splice junctions, how is it therefore aligning less reads that bowtie alone!?
With some parameter adjustments (i.e. --best flag) we are able to get up to 70% reads mapped using bowtie alone but in doing this we are not able to map the splice junction reads and the --best flag cannot be set for bowtie when running it through tophat.
Does anyone know if it is possible to get tophat to output only the splice juntion reads (i.e. everything bowtie would not have aligned) so they can be added to the bowtie output, or is there a fairly simple way of altering the bowtie parameters when running it within tophat?
As you might have guessed, I am only just begining my journey into the worderful world of bioinformatics so go easy on me!
Any help or advise would be greatly received!!
Huw
With default settings tophat is able to align about 35% of reads, whereas bowtie on default is able to align 53%!!
I'm assuming that tophat first runs bowtie then tried to align reads that span exon splice junctions, how is it therefore aligning less reads that bowtie alone!?
With some parameter adjustments (i.e. --best flag) we are able to get up to 70% reads mapped using bowtie alone but in doing this we are not able to map the splice junction reads and the --best flag cannot be set for bowtie when running it through tophat.
Does anyone know if it is possible to get tophat to output only the splice juntion reads (i.e. everything bowtie would not have aligned) so they can be added to the bowtie output, or is there a fairly simple way of altering the bowtie parameters when running it within tophat?
As you might have guessed, I am only just begining my journey into the worderful world of bioinformatics so go easy on me!
Any help or advise would be greatly received!!
Huw
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