Human Transcriptome In Colourspace?

Question

[Huw]

We are trying to map human RNA-seq data from SOLiD platform to the human HG19 reference genome using both Tophat and Bowtie. However as bowtie cannot cope with slice juntions we would like to use bowtie to map to a human transcriptome reference file but cannot find a colourspace version of the human transcriptome available online. Does anyone know where we could find a copy (or maybe a software program that would allow us to create our own?)

Thanks

Huw

Answer 1

[Fred]

Bowtie cannot cope with splice junctions directly, but if I am not wrong TopHat can (and it uses bowtie by the way).

If you want to build your own transcriptome index, you can download transcripts from Ensembl ( ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens/cdna/ )and build your bowtie index with it. But I think you will not be able to map all the junction reads, as you will not capture all the possible alternative splicing events.

[Huw]

Thank you for your response, the reason I ask is that we are finding that Bowtie is mapping a higher proportion of reads than Tophat (despite tophat using bowtie in its mapping step) and wondered if bowtie to transcriptome would be a better way of assessing transcript levels between samples. At least initially, finding alternative transcripts is not a priority.

[Fred]

In this case, you may try to build your own colorspace transcriptome index with bowtie-build:

bowtie-build -C cdna.fa hg19Cdna

[Huw]

Great thank you, hadn't thought of this. Fingers crossed!

Answer 2

[Satyajeet Khare]

I use following command.

tophat -C -p 10 --bowtie1 -G ./gene.gtf --transcriptome-index=./transcriptome_index_Colorspace/gene ./genome_index_Colorspace/genome

Not sure if the outputs of these commands are different.