hsun3163
hsun3163
Hi Wanding, thank you for developing the package in place of Minfi. I have encountered an error trying to annotate the methylation data: While analyzing a dataset for HM450 Human...
(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)...
This is a reminder to add `if ["chr","start","end"] in region: region.remove(["chr","start","end"])` in the genotype formatting notebook when the jupyterserver is avaible again.
This ticket is dedicated to problem 8 in #412. To records potential optimization options _________________________________________________________________ 1. reducing reuse of unneeded data. At the moment, full rows of the query table...
 To generate the annotation in the above visualization, three types of annotation were used, all came from the built-in annotation of annotatr package `CpG Annotations`: Current: Given by the...
It is rather common that, for tasks with a lot of subtask(10000+) , sos process will be interrupted due to all sorts of reasons on the cluster, namely kicked out...
1. When requested mem = 50G, the run fails saying not enough mem ``` ============================================================== qname csg2.q hostname node88 group hs3163 owner hs3163 project NONE department defaultdepartment jobname job_t49524335528fbed8 jobnumber...
1. inconsistance chromosome naming convention between phenotype_per_chrom list and plink_per_chrom_list, wonder how this happened. 2. File name too long... should real change the default naming convention of A+B 3. Memory...
Examplify by chrom 21, although both runs recognized the same dimension of input: beta ``` cis-QTL mapping: nominal associations for all variant-phenotype pairs * 655 samples * 3211 phenotypes *...
I wonder if the following script can be changed to get rid of setwd so that the wd will not be messed up so easily and give us a headache....