hsun3163

There are two scenario of the lost of some snps 1. by the cugg allele_qc function, exemplify by following msg ``` /home/hs3163/miniconda3/lib/python3.9/site-packages/cugg/utils.py:27: UserWarning: There are SNPs 810: REF:ALT = ALT:REF....

Following error occurs when running methyl for chrom21. Shall take look at `` ``` Traceback (most recent call last): File "/mnt/vast/hpc/csg/molecular_phenotype_calling/tmpi874vmi3/singularity_run_38369.py", line 15, in phenotype_df, phenotype_pos_df = tensorqtl.read_phenotype_bed(expression_bed) File "/opt/conda/lib/python3.8/site-packages/tensorqtl/core.py",...

The number of rows in the input of tensorQTL for eqtl is 20000+ while for sqtl is +200000, However, the number of rows in the output of tensorQTL for eqtl...

Sample duplication issue in ROSMAP RNASeq and Genotype

3

This serves as a reminder of the Questions to be answered, @Rhopala will make a comprehensive description of the scenario later on. @gaow please correct me if I got the...

leafcutter_norm output produce data that should not be there

2

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_bam_list_intron_usage_perind.counts.gz_phenotype_file_list.txt #chr #dir chr12 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr12 chr16 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr16 chr21 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr21 chr7 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr7 chr22 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr22 chr14 output/leaf_cutter/xqtl_protocol_data_bam_list_intron_usage_perind.counts.gz.qqnorm_chr14 chr1...

Misspecification gtf in STAR_outline MWE of RNA_calling,

9

Originally, to generate the STAR_Index and RSEM_index, the same gtf, the gtf prior to collapse by gene should be used. However, as we decided to do STAR_indexing on the fly,...

Problem with download_hg_reference

1

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_testing/finalizing/reference_data$ GRCh38_ful...lus_decoy_hla.fa: : ERROR: download_hg_reference (id=c29278acf831fdde) returns an error. ERROR: [download_hg_reference]: [0]: --------------------------------------------------------------------------- RuntimeError...

Norminal cis-windows for mQTL using TensorQTL

5

As noted in point 1 here: https://github.com/broadinstitute/tensorqtl/issues/68 > there will be >400K CpG sites in the data compared to >20K genes. What would you suggest be a good cis_window for...

Update on the dosage genotype to accommodate imputation genotype

7

1. pgen can store and output dosage from the imputed genotypes 2. our existed pipeline should be able to works on pgen/bim/fam file sets, which leads to the minimum amount...

The order of the command generated by command generator is not stable

1

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 | uniq -c 8 sos run /home/hs3163/GIT/xqtl-pipeline/pipeline/gene_annotation.ipynb region_list_generation \ 8 sos run /home/hs3163/GIT/xqtl-pipeline/pipeline/gene_annotation.ipynb annotate_coord \ 8 sos run /home/hs3163/GIT/xqtl-pipeline/pipeline/TensorQTL.ipynb cis...