User: sidwell

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sidwell10
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3 years, 10 months ago
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Posts by sidwell

<prev • 9 results • page 1 of 1 • next >
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Comment: C: RNAseq RSEM and featurecounts
... I thought multi-mapping reads was about a read which is mapping at multiple locations. But here my read map at ONE position. But this position is corresponding to multiple transcripts. ...
written 15 days ago by sidwell10
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RNAseq RSEM and featurecounts
... I use RSEM to count abundance of each transcript after alignment with STAR and featureCounts to count abundance of each transcript after alignment with Bowtie. My question is, if a read map on a given location of the genome, but at this location, there are multiple transcripts overlapping : How R ...
alignment rna-seq written 15 days ago by sidwell10 • updated 15 days ago by igor11k
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Comment: C: CellRanger in cluster mode with slurm template
... Thanks for you time, it would be great if you could try it out but I understand if you don't find the time. I will try to check my slurm configuration in details. I found all links on this page of 10x : https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/tutoria ...
written 8 months ago by sidwell10
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Comment: C: CellRanger in cluster mode with slurm template
... I tried without `#SBATCH --nodes=1 --ntasks-per-node=__MRO_THREADS__`. I am using the example data for cellranger : > This guide outlines how to perform the analysis, and what results 10x assays and software produce using data from a recent Nature publication “Single-cell transcriptomes of the ...
written 8 months ago by sidwell10
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Comment: C: CellRanger in cluster mode with slurm template
... Ok but still, it doesn't explain why it is faster in `job submission mode` on 1 compute node and slower in `cluster mode` on 5 compute nodes. With same parameters. It should be faster in `cluster mode` on 5 nodes. It is what they are saying in documentation : > Cell Ranger can be run in `cluster ...
written 8 months ago by sidwell10
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Comment: C: CellRanger in cluster mode with slurm template
... After verification, my cluster is allow to submit sub-jobs. I tried with your way (write the cellranger command in a bash script and wrap it), the only difference I see is that the `mrp` process (which is the process that submit all jobs) run on a compute node instead of running on head node. But ...
written 8 months ago by sidwell10
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Comment: C: CellRanger in cluster mode with slurm template
... Thanks for you answer. >Your cluster does need to allow SLURM jobs to submit sub-jobs Do you mean allow multiple jobs by node ? Or allow jobs to be submitted from a compute node ? I will try your way ...
written 9 months ago by sidwell10
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CellRanger in cluster mode with slurm template
... If someone has already manage to run cellRanger with Slurm, maybe you can help me : Until now, I was running CellRanger on a cluster, on a single node of 512Go RAM. For a dataset of 6,7k cells and 90k reads/cell, `cellranger count` function takes 7h30. I can dispose of 5 nodes of 512Go RAM. I ...
rna-seq written 9 months ago by sidwell10
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Haploview Aggressive Tagging no output
... Hi, I'm trying to do an aggressive tagging on 1000G datas with a list of markers java -jar Haploview.jar -n -out output -plink chr1.ped -map chr1.map -info info_file ...
haploview output tagging written 3.8 years ago by sidwell10

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