Tingting Shao

ArchRProject

1

**Code** > ArrowFiles > 'arrows''D19-13000.arrow''D19-8612.arrow''D19-8613.arrow' > brain1 ...... test all three of them, all three of them can be created successfully. However: with all the ArrowFiles, it shows error: >...

add_cor_scores

4

Hi, I ran into error when running ```python net = snap.tl.init_network_from_annotation(regions, anno_file =snap.genome.hg38, upstream = 250000, downstream= 250000, id_type = 'gene_name', coding_gene_only = True) net = snap.tl.add_cor_scores(net, gene_mat=gene_mat, peak_mat=peak_mat, select=None,...

Hi, Could I please ask if there is one way to color the cells with openness of a certain region. For example, if I found a regions is very interesting,...

Hi, I ran into unexpected error never met before with the established pipeline, not sure why ```python rule get_consensus_peaks: input: narrow_peaks_pkl=os.path.join(config['work_dir'], "030results_cistopic/010consensus_peak_calling/MACS/narrow_peaks_dict.pkl"), output: consensus_regions=os.path.join(config['work_dir'], "030results_cistopic/010consensus_peak_calling/consensus_regions.bed") run: narrow_peaks_dict=pickle.load(open(input.narrow_peaks_pkl, 'rb')) print("-------narrow-peaks-dict--------") print(narrow_peaks_dict)...

models

2

Hi, The job: ```bash shell: """ pycistopic topic_modeling mallet \ -i {input.obj_pkl} \ -o {output.topic_pkl} \ -t 2 5 10 20 30 35 40 45 50 55 60 65 70...

snapatac2.tl.diff_test

2

Hi, I generated gene-activity matrix with function make_gene_matrix, could I please ask if the function snapatac2.tl.diff_test can be used to impute the differentially accessible genes? Thanks, tingting

snap.tl.macs3

1

Hi, When I ran the step snap.tl.macs3, the return dictionary is None, could I please ask the reason behind this? I also called peaks in pycistopic, it returned the value,...

localrule region_to_gene

5

Hi, Before it worked fine, but this time, it shows error: ```bash localrule region_to_gene: input: /lustre1/project/stg_00079/students/tingting/data/sun/snap2_allfragments/08/080results_scenicplus_pycistopic/ACC_GEX.h5mu, /lustre1/project/stg_00079/students/tingting/data/sun/snap2_allfragments/08/080results_scenicplus_pycistopic/search_space.tsv output: /lustre1/project/stg_00079/students/tingting/data/sun/snap2_allfragments/08/080results_scenicplus_pycistopic/region_to_gene_adj.tsv jobid: 10 reason: Missing output files: /lustre1/project/stg_00079/students/tingting/data/sun/snap2_allfragments/08/080results_scenicplus_pycistopic/region_to_gene_adj.tsv threads: 20 resources: tmpdir=/tmp...

Memory issue even after bigmem

7

Hi, I am running the step ```python rule imputed_acc: input: obj_pkl=os.path.join(config["work_dir"], "030results_cistopic/cistopic_obj.pkl"), flag=os.path.join(config['tmp_dir'], 'flags/topic_annot.done'), output: imputed_acc_obj=os.path.join(config["work_dir"], '030results_cistopic/040dars/imputed_acc_obj.pkl'), run: from pycisTopic.diff_features import impute_accessibility import numpy as np cistopic_obj = pickle.load(open(input.obj_pkl, 'rb'))...

results not ideal

6

Dear, This is my first try with WSInfer, and I would like to ask for more features and advice on it. The aim of the project: (1) to identify metastasis...