Hi all,
I have 50bp paired illumina reads which I have aligned with tophat (default parameters).
The alignments look reasonable in IGV, or UCSC browser.
I have run scripture on the tophat output, and I get a list of isoforms that look reasonable, if not verbose.
However, when I run cufflinks I get very spotty connectivity.
I am trying to attach a screenshot, which shows at the top, the split alignments of tophat, then the predicted transcripts of scripture, and below that, before the reference gene annotations there is the cufflinks output.
Has anyone else seen cufflinks output that is disconected like this? Any ideas on how to improve the results?
I have run scripture, and cufflinks on the same file.
(the screenshot attempt didn't work out)
The image I tried to attach has been posted here instead:
I have 50bp paired illumina reads which I have aligned with tophat (default parameters).
The alignments look reasonable in IGV, or UCSC browser.
I have run scripture on the tophat output, and I get a list of isoforms that look reasonable, if not verbose.
However, when I run cufflinks I get very spotty connectivity.
I am trying to attach a screenshot, which shows at the top, the split alignments of tophat, then the predicted transcripts of scripture, and below that, before the reference gene annotations there is the cufflinks output.
Has anyone else seen cufflinks output that is disconected like this? Any ideas on how to improve the results?
I have run scripture, and cufflinks on the same file.
(the screenshot attempt didn't work out)
The image I tried to attach has been posted here instead:
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