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Hi,
First of all, I want to commend you on creating an impressive tool—great work! I have a few comments and questions that I hope can help clarify some aspects:
1. MAF vs. EAF in GWAS Datasets…
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Dear @yu-1011 @liusihan @Fefe-W
Thanks for your the great paper!
The EAS eQTL/sQTL summary data download urls in the paper are broken. How to download EAS QTL summary data?
Thanks in adva…
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As demostrated below:
```
hs3163@node57:/mnt/vast/hpc/csg/snuc_pseudo_bulk/eight_celltypes_analysis$ cat /mnt/vast/hpc/csg/snuc_pseudo_bulk/eight_celltypes_analysis/8_celltypes_script_3 | grep sos …
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after running leafcutter on the STAR_output of xqtl_protocol_data, the output is:
```
hs3163@node74:/mnt/vast/hpc/csg/xqtl_workflow_testing/finalizing$ cat output/leaf_cutter/xqtl_protocol_data_ba…
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When I try to run the map_leafcutter_cluster_to_gene part for post-processing, it gives me this error..
```
FATAL: could not open image /restricted/projectnb/casa/xqtl-pipeline/container/singul…
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@hsun3163 I'm raising this issue here, for there are problems recently reported due to obsolete or incomplete minimal working example commands as a result of changes made. I'll make a TODO list in thi…
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The codes below are quoted from the notebook.
```
sos run splicing_calling.ipynb psichomics \
--cwd psichomics_output/ \
--samples sample_fastq_bam_list\
--splicing_annotation hg38_su…
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While running `sos run pipeline/reference_data.ipynb download_hg_reference --cwd reference_data` in the login node, following error occurs.
```
hs3163@csglogin:/mnt/vast/hpc/csg/xqtl_workflow_test…
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From the step of `rnaseqc_call`, 8 bam files returned with an error message indicating `BAM file shares no contigs with GTF`
and this error message is preventing moving forward to the next step for…
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Since for `susie_rss()` (for GWAS data integration, not for xQTL where we use `susie()`) we decide to use the `polyfun::finemapper.py` wrapper, we can implement the FINEMAP method in it for free (`--m…