User: roy.granit
roy.granit • 810
- Reputation:
- 810
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- Trusted
- Location:
- Israel/LabWorm
- Website:
- http://roygranit.me/
- Twitter:
- rgranit
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 weeks, 2 days ago
- Joined:
- 5 years, 7 months ago
- Email:
- r*********@gmail.com
I'm a co-founder & CTO at LabWorm a crowd voting platform that enables scientists to discover the best & newest online research tools. Previously I explored pathways that determine intratumoral heterogeneity using high-throughput molecular biology & bioinformatics. My personal website.
Posts by roy.granit
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... Thanks, it ran OK with just `cutadapt` ...
written 28 days ago by
roy.granit • 810
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... Trim Galore uses Cutadapt in the process, but nothing shows in the log :( just this
> This is cutadapt 1.18 with Python 3.6.6 Command line parameters: -j 1
> -e 0.1 -q 33 -O 1 -a CTGTCTCTTATA ./data/TCOC23_S14_R1_001.fastq.gz Processing reads on 1 core in single-end mode ...
Will add the cod ...
written 28 days ago by
roy.granit • 810
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... I'm using Trim Galore to process RNAseq and in one of the samples in get this error:
> Cutadapt terminated with exit signal: '24'. Terminating Trim Galore
> run, please check error message(s) to get an idea what went wrong...
This is the code I've used:
../TrimGalore-0.6.4/trim_galore . ...
written 28 days ago by
roy.granit • 810
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... The goal is to check how heterogeneous each cluster is.. one could take the correlation between all cells but that would not be very interesting since most genes do not change or are not expressed. ...
written 4 months ago by
roy.granit • 810
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... Thanks that was my thinking as well. Is there another way of showing a measure of how cells in a given cluster are similar to each other?
I initially took the distances of all cells from the center of the cluster.. but I guess this is just another view of the clustering ...
written 4 months ago by
roy.granit • 810
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... I'm working on single cell expression data using Seurat and have generated a umap and performed clustering of the data.
Now I was asked if there is a way to plot / calculate the distance between all cells in a given cluster, and was suggested to take the vector of each cell and run a formula like t ...
written 4 months ago by
roy.granit • 810
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Comment:
C: What does "Quadratic sum" mean?
... Thanks, but the problem that the forum is not that active so I could not find an answer there.. ...
written 6 months ago by
roy.granit • 810
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... I've used inferCNV to predict CNVs based on single cell expression data, and now I wish to calculate the "CNV score" as conducted in [this][1] publication.
It says:
"The CNV score of each cell was calculated as quadratic sum of CNVregion"
The possible values are 0.5, 1.5, 2 - but what does "Quadr ...
written 6 months ago by
roy.granit • 810
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... Hi All,
I suspect that my sample might have dna contamination. Is there a way of telling the fraction of reads mapped to the transcriptome vs genome when using the STAR aligner?
I have used the --quantMode TranscriptomeSAM flag so I guess that can use samtools to count the number of reads mapped t ...
written 6 months ago by
roy.granit • 810
• updated
6 months ago by
grant.hovhannisyan • 1.9k
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... Thanks. Ended up using this code after converting my .mate1 files into bam using picardtools ...
written 6 months ago by
roy.granit • 810
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