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I successfully ran the below code to generate the cis eQTL results; however, when I was uploading the results to a MySQL database I received a warning that one of the lines was truncated for 'se'. Th…
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From the stderr:
```
/home/hs3163/miniconda3/lib/python3.9/site-packages/cugg/utils.py:27: UserWarning: There are SNPs 960: REF:ALT = ALT:REF. They will be removed.
warnings.warn("There are SNPs …
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In the LD file, the snp chr17:63476980_T_C have a ref = T while alt = C. (bim file last 2 columns order is alt, ref )
```
hs3163@csglogin:/mnt/vast/hpc/csg/molecular_phenotype_calling/LD/output_npz…
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Were the susieRSS results saved with the LD they depends upon, the file size for each of them are as follows for the non-imputed one:
```
hs3163@node95:/mnt/vast/hpc/csg/xqtl_workflow_testing/susi…
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**Script used:**
### Residual Expression: sQTL
```
sos run /restricted/projectnb/casa/xqtl-pipeline/pipeline/covariate_formatting.ipynb compute_residual \
--cwd /restricted/projectnb/c…
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While testing the commonly used `stephenlab.sif` the following error occurs. The same error also occurs on other variants of the `stephenlab.sif`, including the `stephenlab_flashier.sif`. This is stra…
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In the output of leafcutter for ROSMAP, ~600 out of ~200000 of the rows are duplicated, exemplified by
```
[skandoi@scc4 batch_all]$ cat /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_ou…
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```
/home/hs3163//sQTL_data_intergration.21.yml False False
Total number of sumstats: 1
{'/home/hs3163//sqtl_chr21.txt': {'ID': 'GENE,CHR,POS,A0,A1', 'CHR': 'chrom', 'POS': 'pos', 'SNP': 'variant_…
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Following commands:
```
sos run /restricted/projectnb/casa/xqtl-pipeline/pipeline/TensorQTL.ipynb cis \
--genotype_file /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/PDP_rnaseqc/ROSMAP_NIA_WG…
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Hi,
Below is shows the number of probes having NA:
`hs3163@node60:/mnt/vast/hpc/csg/xqtl_workflow_testing/methyl/sesame_2$ cat ROSMAP_arrayMethylation_covariates.sesame.methyl.M.tsv | grep NA | w…