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Is it necessary to de-redundant the resulting transcript model? #257
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Dear @wjcre2023 Could send a command line you used? Best |
Dear @andrewprzh Also it seems that the.gff file is still not available in 3.6.1, I uploaded a log file. |
Dear @wjcre2023 Yes, I think the main reason is P.S. You log shows an error caused by duplicated ids in your reference annotation. Best |
Dear @wjcre2023 The ID should be unique for all features, even for exons belonging to a single CDS.
So that's why gffutils library that IsoQuant uses to convert GFF to gene database freaks about this. I think it's better to modify our annotation. It is possible to ignore these warnings (i.e. convert GFF to database with other options), but then the outcome is not predictable. Best |
Dear@andrewprzh |
Dear @andrewprzh |
Dear @wjcre2023 The parameters looks OK. Could you send me GTF records of these two transcripts? Best |
Dear@andrewprzh |
Dear andrewprzh
I ran all the samples together and ended up with a transcript model .gtf file. However, many new but very similar transcripts have been found in IGV with the same number of exons, with only a few hundred bp difference in the length of some exons. Do these require further removal of redundancy? Because this is most likely due to degradation of the 5 'end.How to deal with this situation? Should reads be de-redundant before quantitative and transcriptional modeling?
best wishes
jie
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