Question: Human Transcriptome In Colourspace?
2
gravatar for Huw
7.9 years ago by
Huw30
Huw30 wrote:

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

tophat rna bowtie transcriptome • 2.0k views
ADD COMMENTlink modified 3.0 years ago by Satyajeet Khare1.3k • written 7.9 years ago by Huw30
3
gravatar for Fred
7.9 years ago by
Fred710
Paris, France
Fred710 wrote:

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.

ADD COMMENTlink written 7.9 years ago by Fred710
1

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.

ADD REPLYlink written 7.9 years ago by Huw30

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

bowtie-build -C cdna.fa hg19Cdna

ADD REPLYlink written 7.9 years ago by Fred710

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

ADD REPLYlink written 7.9 years ago by Huw30
0
gravatar for Satyajeet Khare
3.0 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Satyajeet Khare1.3k
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