Help for mapping with 454 data

[lixiangru]

Hi all!
Is any mapping tools designed for 454 cDNA data?
BWA seems not work well with 454 data.
Hope for some suggestion.

[flxlex]

If you can get access to the Roche tools, gsMapper might be a tool to try.

[lixiangru]

If you can get access to the Roche tools, gsMapper might be a tool to try.

Thanks you. I have account for gsMapper. But it seems that gsMapper doesn't account for junction reads but I hope those included.

[maubp]

What do you mean by junction reads? Do you mean mapping transcriptome reads in an intron/exon aware way?

[lixiangru]

What do you mean by junction reads? Do you mean mapping transcriptome reads in an intron/exon aware way?

Yes.take splicing into account. some reads may be mapped to the junction of two exons separated by an intron on the chromosome.