hsun3163

This ticket document a list of sos problem that I am not able to fix. - [ ] 1. #296 - [ ] 2. #378

How to define cpg site at overlapping cis windows?

7

As per our discussion, we will define the molecular phenotype object of cpg site by a cis window around the TSS of each gene. However, one of the problems of...

8 samples of ROSMAP needs excessive amount of mem: 128GB

1

During the RNASeqc, Small number of jobs aborted due to requesting more memory Star works fine. Outliers issue?

v_simple of MASH module not recognizing the container

6

while running: ``` nohup sos run pipeline/mashr.ipynb mash \ --container containers/stephenslab.sif \ --output_prefix Ast_Exc_Inh_Mic_OPC_Oli \ --data output/Ast_Exc_Inh_Mic_OPC_Oli.rds \ -s force -J 20 -q csg -c csg.yml --cwd MASH_6_celltypes ``` Following...

Current status and potential improvement of command generators

1

For the command generator to be organized into a protocol-module structure similar to other sections, this ticket will outline its current status and some potential caveats. Current status: There are...

Command generators will not run without -n (dryrun option)

2

It should be brought to attention that. For our command generator, if run without `-n`, following error will occurs: ``` ERROR: [sample_match (sample_match)]: [sample_match]: Output target /mnt/mfs/statgen/snuc_pseudo_bulk/eight_tissue_analysis/MWE/QTL_association/output/data_preprocessing/MWE/sampleSheetAfterQC.filtered.txt does not exist...

31 genes was excluded in the per gene result for APEX

2

For 13906 number of genes in input. 31 was not included in the APEX per gene result. All of the 31 were in chrome 22. Reason unknown. This may explain...

Mandatory for GTF to be gene-collapsed before entering the annotation_coord for phenotype file

3

As it turn out. The gene.gtf file provided in out snuc study is exon based instead of gene based. This create a lot of records with duplicates gene IDs but...

A page to outline the input format for each of the modules

1

I think it would be wise to add a page to outline the input requirement for each of the modules. An example for such is: https://corbinq.github.io/apex/doc/input_files/ Actually I would like...

guard against strange snp name

1

guard against the strange variant name, also add back the parameter to filter x for the LD matrix computed on the fly