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Splice aware RNA-seq analysis
Hi,
I have RNA-seq data generated on ABI's SOLiD platform (i.e. colorspace) and have analyzed the basics using the bowtie aligner. Now I want to use a splice-aware mapper to map reads to exon junctions.
I noticed that Tophat doesn't yet support SOLiD data.
Does anyone have a suggestion ab out how to go about this?
It seems that there are some bugs when using Bioscope output for Cufflinks - has this worked for anyone?
Should I convert my data to fastq and work from there or am I going to lose too much accuracy?
Any help would be appreciated!
Thanks,
Ilana
I have RNA-seq data generated on ABI's SOLiD platform (i.e. colorspace) and have analyzed the basics using the bowtie aligner. Now I want to use a splice-aware mapper to map reads to exon junctions.
I noticed that Tophat doesn't yet support SOLiD data.
Does anyone have a suggestion ab out how to go about this?
It seems that there are some bugs when using Bioscope output for Cufflinks - has this worked for anyone?
Should I convert my data to fastq and work from there or am I going to lose too much accuracy?
Any help would be appreciated!
Thanks,
Ilana