Open khushi0810 opened 3 months ago
Can you check some intermediate results? Such as how many cells did you get under filtered_Matrix folder or any other output? I guess some of your filtering parameters may be too stringent, like min_frac_peak set as 0.5.
Hello,
Thank you so much for your reply. I am attaching my results under filtered_matrix folder. Should I try increasing the threshhold ?
Thanks barcodes.txt features.txt
No, you need to decrease your thresholds, for instance, min_uniq_frags to 2000, min_frac_peak 0.25. You can increase max_frac_mito to 0.15 or 0.2.
Thank you so much. I changed the threshholds and was able to resolve this error but bumped into another error
Error in FindNeighbors.Seurat(seurat.obj, reduction = "pca", dims = 1:30, : More dimensions specified in dims than have been computed Calls: FindNeighbors -> FindNeighbors.Seurat Execution halted
Should I change the nReduction parameter ?
Error: Cannot find 'active_clusters' in this Seurat object Execution halted Report generation Done!
Do I need to change this parameter ? K_CLUSTERS = 0.2 ## the number of cluster (in integer) or the resolution parameter (in float) for louvain algorithm (implemented by seurat)
Thank you !
Not sure what exactly happened. Have you checked the outputs? I guess you probably ended up too few number of cells.
Hello Wenbao @wbaopaul ,
I am using v1.5.1 on one of my samples , and I'm using scATAC-pro reprocess because I have my bam files from cell ranger and then using scATAC-pro downstream .
I am running on HPC as a batch job. I am attaching my log file , configure file as well as my script for you reference.
Any suggestions are highly appreciated.
Thank you Khushi reprocess_cellranger_output.log configure_user.txt
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module load singularity/3.9.9
cd /project/bioinformatics/JLee_lab/s227606/scATAC/NONP
singularity exec --bind /project/bioinformatics/JLee_lab/s227606/scATAC -H /project/bioinformatics/JLee_lab/s227606/scATAC/NONP --cleanenv /project/bioinformatics/JLee_lab/s227606/scATAC/NONP/scatac-pro_latest.sif scATAC-pro -s reprocess_cellranger_output -i /project/bioinformatics/JLee_lab/s227606/scATAC/files/BL51_NP/outs/possorted_bam.bam,/project/bioinformatics/JLee_lab/s227606/scATAC/files/BL51_NP/outs/fragments.tsv.gz -c /project/bioinformatics/JLee_lab/s227606/scATAC/configure_user.txt
singularity exec --bind /project/bioinformatics/JLee_lab/s227606/scATAC -H /project/bioinformatics/JLee_lab/s227606/scATAC/NONP --cleanenv /project/bioinformatics/JLee_lab/s227606/scATAC/NONP/scatac-pro_latest.sif scATAC-pro -s downstream -i /project/bioinformatics/JLee_lab/s227606/scATAC/NONP/output/filtered_matrix/MACS2/FILTER/matrix.mtx -c /project/bioinformatics/JLee_lab/s227606/scATAC/configure_user.txt
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