xqtl-protocol
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StatFunGen
Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
sQTL association analysis in job `8eaa4402df95e92a` on opcenter 23.22.157.8 showing > ERROR: cis_1 (id=8eaa4402df95e92a) returns an error. > ERROR: [cis_1]: [0]: > Failed to execute python /home/bst2126/output/cis_1_0_258db4a1.py > exitcode=139, workdir=/home/bst2126/data,...
Raised today by @Bale4 who seems to have to manually adjust / rearrange columns for phenoIDFile when performing sQTL analysis. I think we should generate this file from our pipeline,...
Running alignment with the STAR wasp option creates *toTranscriptome.out_wasp_qc.bam files. When running RSEM, the code expect the files to not include "_wasp_qc" in the name, causing an error.
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/singularity/bioinfo.sif: SIF image /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif is corrupted: wrong partition size...
(py3.11) [sunh14@lc03e22 ~]$ cd /sc/arion/projects/CommonMind/roussp01a/snmulti_QTL/working (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_hg_reference --cwd ../input/reference_data & [1] 189132 (py3.11) [sunh14@lc03e22 working]$ sos run pipeline/reference_data.ipynb download_gene_annotation --cwd ../input/reference_data & [2] 189133 (py3.11)...
@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...
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...
@hsun3163 this ticket keeps track of modules that I (re)reviewed : at this round I mostly make all the changes myself and try to finalize everything. Every time I finalize...
There are some "*" (which means a deletion) in snp file will cause the error `Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 42 (char '*') not in lookup table` That...
I am reproducing the MASH pipeline, and I found the result of `mashr` is different from the available results (produced by Hao), the code in this step is > library(mashr)...
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Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium