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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
MIT License
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questions: de-novo transcriptome assembly #664

Open bernt-matthias opened 6 years ago

bernt-matthias commented 6 years ago

The Megakaryocyte_rep2 data is much smaller than the other samples. Is this intended? In https://www.ncbi.nlm.nih.gov/sra/?term=SRR549358 the original data of the two samples is about the same size. It seems unlikely that down sampling created this bias. Maybe some error happened while downloading / uploading?

StringTie is can estimate transcript abundances on its own. Then what is the intension of using featurecounts+DeSeq2 instead of directly using DeSeq2? If Stringtie is given the gff then one can configure to output DeSeq2 compatible output. I guess its just that when the tutorial was created this possibility was not yet available...

bernt-matthias commented 6 years ago

In my first experiment with the current hisat2 and stringtie I got only one transcript for chr19 which is odd since the tutorial states that the input data is downsampled for chr19. For all other chromosomes more transcripts are found.