read to transcript relationship in final polished transcriptome.fq

[alexyfyf]

Hi team,

I am able to run the whole process of rattle and obtain a transcriptome.fq file at the end.
My understanding is that this file is the final transcriptome after re-merging similar clusters and redistributing some sub-clusters. However, the header of the fastq file cannot be easily related to the first-pass cluster information (read-cluster mapping).
Is it possible to add some intermediate file (or how we can get it) so that we can look at read-transcript mapping after all steps are finished? Particularly, which reads/first pass clusters are discarded or redistributed.

Thank you for the help.
Cheers,

[eileen-xue]

Hi,

We provide an update for RATTLE.

The new parameter '--summary' for the polish step can print a summary of the relation between the transcript clusters from the clustering step and the new polish transcriptome clusters. More detailed information can be found here.

You can use the correct.fq to find the reads we used to generate the consensi and transcriptome, the gene/transcript cluster ids are also the same as the clustering step. 'uncorrect.fq' stores the reads which are discarded.

I hope this helps you solve your problem.

Cheers,
Eileen

[alexyfyf]

Thanks so much. I'll try it now.