grennfp

RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter

1

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.

I was working on running `gene_annotation.ipynb map_leafcutter_cluster_to_gene` and had some issues getting the notebook to run. I commented on another issue which I thought could be [related](https://github.com/cumc/xqtl-pipeline/issues/394). The main issue...

Bug in bulk_expression_QC.ipynb RLE candidate outlier output

1

I've been testing the bulk_expression_QC.ipynb notebook to conduct QC on a 559 sample RNASeq dataset. All three parts (Hierarchical clustering, D-statistic correlations, RLE) produce candidate outliers, but none of the...