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Dear Eduardo,
Thank you so much for this extremely useful program, SUPPA2.
I have been running your program on my RNA-seq dataset (2 conditions in triplicates) for the analysis of alternative spli…
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Hello,
I was wondering if rounding the quantification be justifiable in regards to the "correctness/accuracy" of the data? Specifically I'm running some pipeline that requires integers, from readin…
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### Description of bug
I have been running Philosopher 4.0.0 since August, and I was unable to reproduce a run that I had generated about a month ago due to
1. Philosopher not reading in the sp…
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* spladder version: latest
* Python version: 3.6.8
* Operating System: linux
Hello guys,
An issue encounter to me, I don't know how to fix it.
When I use spladder build mode to detect alter…
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Dear SUPPA developers,
first of all: thanks a lot for providing your nice tool set!
I have one feature suggestion though:
Since you have now included a script for the differential analysis of s…
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Hi,
I am newly associated with transcriptomics and Trinity. From the paper "https://dx.doi.org/10.1038%2Fnprot.2013.084" i have come to know that Trinity also can assemble the isoforms. For downstrea…
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I have added gene_name s to the original Refseq genome annotation file from UCSC, but when I run Stringtie and Ballgown, there are some genes/transcripts that don't have their gene_name added and only…
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Hi,
I am trying to run ASGAL and I am interested: how the files in the logs/ASGAL folder are produced and what do they mean? In the genomewide mode are they produced for each gene in the genome ann…
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For a metatranscriptomics project I plan to use SPAdes in the SqueezeMeta pipeline. This pipeline has metaSPAdes as its standard method, since it’s a pipeline designed for meta-omics. I was wondering …
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Dear All,
I am having some troubles in using psichomics. I would like to use a combined reference with events retrieved from VAST database and from SUPPA. When I process the 2 annotations with _par…
ghost updated
4 years ago