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Hello,
I have about 340 RNA seq data sets, what do you recommend is the best method for understanding shared alternatively spliced transcripts among all the samples?
Specific question:
Whe…
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As gtex have already implement a way to conduct [sQTL analysis](https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl/leafcutter) via tensorQTL and leafcutter.
We can piped what we curre…
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Hello,
I've used DROP on a single sample (Used ~30 normal samples from SRA as reference) and while analyzing results from Aberrant Splicing > Pipeline > Fraser > Results Table. There are several Th…
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Hi,
I performed transdecoder on 13 RNA samples at first, and then included 18 more samples to perform gene prediction with transdecoder. Using the same genome( repeats unmasked), I was able to pred…
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Hi Aaron and Brent,
On the the gemini main page you sate "GEMINI is very strict about adherence to VCF format 4.1." However, with the recent update to GATK4 the default, and unmodifiable, output of H…
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This was run using the latest docker run, the error appeared when I used the `--test `
```
DRIMSeq testing for each AS event type
Traceback (most recent call last):
File "/usr/local/bin/flair"…
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Hello,
I've been looking through documentation searching for any advice/suggestions on normalization or Quality Control.
Specifically when using quantifySplicing() function using user-uploaded …
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We would like to include splice prediction as one of the facets when determining if a variant is plausibly relevant to diagnosis. This will be a little more complicated than just adding a new category…
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Hi,
Thanks for this useful package.
I'm testing different values for the `avg_reads` parameter, which from the code seems to account for the average number of reads obtained per event across all …
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Hi,
I am new to DROP and blood RNAseq in general, so please let me know if the question was not described properly or other files should be provided.
Thanks!
My dataset : ten bam files from bl…