User: roy.granit

gravatar for roy.granit
roy.granit810
Reputation:
810
Status:
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

<prev • 134 results • page 1 of 14 • next >
0
votes
0
answers
83
views
0
answers
Comment: C: Cutadapt terminated with exit signal: '24'.
... Thanks, it ran OK with just `cutadapt` ...
written 28 days ago by roy.granit810
0
votes
0
answers
83
views
0
answers
Comment: C: Cutadapt terminated with exit signal: '24'.
... 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.granit810
0
votes
0
answers
83
views
0
answers
Cutadapt terminated with exit signal: '24'.
... 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 . ...
rna-seq written 28 days ago by roy.granit810
0
votes
0
answers
200
views
0
answers
Comment: C: distance between cells in scRNA-seq expression data
... 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.granit810
0
votes
0
answers
200
views
0
answers
Comment: C: distance between cells in scRNA-seq expression data
... 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.granit810
5
votes
0
answers
200
views
0
answers
distance between cells in scRNA-seq expression data
... 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 ...
scrnaseq written 4 months ago by roy.granit810
0
votes
0
answers
247
views
0
answers
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.granit810
0
votes
0
answers
247
views
0
answers
What does "Quadratic sum" mean?
... 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 ...
infercnv cnv written 6 months ago by roy.granit810
1
vote
1
answer
272
views
1
answer
Genome vs transcriptome alignement in STAR
... 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 ...
star rna-seq written 6 months ago by roy.granit810 • updated 6 months ago by grant.hovhannisyan1.9k
0
votes
2
answers
207
views
2
answers
Comment: C: How does one count unmapped transcripts ?
... Thanks. Ended up using this code after converting my .mate1 files into bam using picardtools ...
written 6 months ago by roy.granit810

Latest awards to roy.granit

Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 6 months ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Great Question 13 months ago, created a question with more than 5,000 views. For What is the input for clusterProfiler R pack
Popular Question 13 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 13 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 17 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Centurion 20 months ago, created 100 posts.
Popular Question 21 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: About gene id
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 4.8 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: About gene id
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1250 users visited in the last hour