Using Cufflinks with AB SOLiD Data?

[Haneko]

Hi damiankao. For SOLiD data, do you use the full SAM file including all unmapped, unique mapped and multimapped reads? Or do you only use the set that contains the SOLiD-defined unique alignments (best score, and score >4 away from second best)?

EDIT:

I forgot to mention. In the manual, it states that cufflinks is unable to support other operations such as clipping. SOLiD bioscope whole transcriptome analysis includes hard clipping (H) in the CIGAR string for the output. May I ask how you dealt with that?

Thanks!

[damiankao]

I am using Bioscope mapping output .bam files as input into cufflinks. You have to first convert to .sam file, clean it up, and added the strand information by parsing the bitwise flag.

I was able to run this cleaned up version of .sam file through cufflinks with pretty good results. The only problem I am having is that most of the output is not showing any strand information.

I think cufflink is only using strand information for spliced reads and ignoring unspliced read strand? So all the genes assembled with spliced read has strand information, but others don't?

[Haneko]

I'm actually trying to use the BioScope output for RNA-seq for cufflinks now.

In my sam file, it doesn't contain the "XS:A:" flag that is said to be a must to have from the documentation i read for the splice reads. When I ran cufflinks, I was expecting an error, but nothing popped out. Does this mean the flag is not required?

[lgoff]

Has anyone tried to use cufflinks to assemble isoforms from SOLiD RNA-Seq data? Now that Bowtie supports colorspace reads, I am trying to take this output and process the alignments through cufflinks with little success.

I understand that TopHat adds the required XA:i:[+-] tag to the alignments, which I am able to add due to this being a strand-specific library. Whether or not I add this tag myself, when I run cufflinks, no output is reported (other than headers) into the output files.

Anyone had this issue or dealing with transcript assembly in SOLiD? Any help is appreciated...