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Hi there - I'm having some problems running `HaplotypeCallerSpark` on RNA-Seq data.
The tl;dr is that, on some occasions when `HaplotypeCallerSpark` runs out of memory, it finishes successfully, b…
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Hi Alish
I just wanted to say thank you for creating the pipeline. It has been incredibly useful.
I have updated the pipeline to output RNA seq transcript as counts rather than fractions by upda…
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Hi! Thanks for the cool tool!
When I start from estimated read counts from a different pipeline (STAR > featureCounts) should I provide Taiji with raw reads or should I normalise them somehow before …
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**Question**
We are comparing different aligners and quantifiers to see their impacts on the same RNA-Seq raw data. Of course, it took long time to run one run. My guess is that we do not have to r…
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Hi,
I'm trying to install Taiji from the source code in our CentOS server using stack and I'm getting requested to give my github credentials during the installation:
```
[gascui@login02 Taij…
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### Objective: As a user with a pipette, I would like the DCP to process 10x v2 and v3 single-nuclei sequencing data (snRNA-seq) so that I can submit such data to the DCP and view the results in the d…
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For GTEx V7 data we've done imputation and rna-seq normalization, and we have PCA analysis results from Broad. PEER analysis is still running. Once we have the result we should have the material to do…
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To connect the PASS1B-06 DEA results data to the phenotypic data, we need to map each unique `feature_id` (present in the DEA results) to a list of associated `vial_label` (present in the phenotypic d…
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Hi,
I tried your pipeline with default parameters with long reads data (pacbio hq isoforms mapped with gmap) and NGS reads. A lot of my isoseq transcripts/isoforms (exons) were filtered out. See th…
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I am implementing this microtest repository and am wondering what should be placed in the [data path] section in these code blocks:
required_input_files: [data_path]
ngs_input_files: [data…