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Old 01-31-2011, 11:30 AM   #1
bogdan
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Default quantification of transcript level

Dear all,

please could you recommend a bug-free software that computes accurately the expression levels of transcripts in RNA-seq data ? I do encounter major problems with Cufflinks. thanks,

bogdan
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Old 02-03-2011, 09:15 AM   #2
danielr
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I have a program I host at http://sandberg.cmb.ki.se/rnaseq/ which you could try.
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Old 02-03-2011, 12:24 PM   #3
RockChalkJayhawk
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Quote:
Originally Posted by bogdan View Post
Dear all,

please could you recommend a bug-free software that computes accurately the expression levels of transcripts in RNA-seq data ? I do encounter major problems with Cufflinks. thanks,

bogdan

Sorry to disappoint you bogdan, but there is no such thing yet. We are all lerning as we go, both biologically and computationally. The best thing you can do is to select a set of tools, identify the strengths and weaknesses with each, and use good judgement.

What seems to be your major problems with Cufflinks? Just curious..
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Old 02-14-2011, 11:48 AM   #4
bogdan
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Thanks to all for the replies and suggestions. The suite Cufflinks-Cuffdiff-cuffcompare gave many genes as not differentially expressed, when these gene are -- not very sure where the problem was.
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Old 02-14-2011, 11:52 AM   #5
RockChalkJayhawk
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Thanks to all for the replies and suggestions. The suite Cufflinks-Cuffdiff-cuffcompare gave many genes as not differentially expressed, when these gene are -- not very sure where the problem was.
Do two things. First, make an MA plot. Second, make a histogram of fold changes. This might help you explain some things.
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Old 08-18-2011, 07:38 PM   #6
chenjiapeng
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Thanks to all for the replies and suggestions. The suite Cufflinks-Cuffdiff-cuffcompare gave many genes as not differentially expressed, when these gene are -- not very sure where the problem was.
Have you found the problem now? I superviser recommend me to go to Galaxy for transcript quantification by RNA-Seq, but Galaxy use Cufflinks-Cuffdiff-cuffcompare. In the next few days, I will also try to figure out how Cufflinks-Cuffdiff-cuffcompare works.
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Old 06-19-2018, 09:04 AM   #7
ptdtan
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We have our own tool: Nora, which will be released freely for academic in June 2018. You can see the benchmark with Kallisto, RSEM, and Salmon here: https://bioturing.com/nora
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