User: roy.granit

gravatar for roy.granit
roy.granit800
Reputation:
800
Status:
Trusted
Location:
Israel/LabWorm
Website:
https://labworm.com/
Twitter:
rgranit
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 2 days ago
Joined:
5 years, 1 month 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 • 128 results • page 1 of 13 • next >
0
votes
0
answers
158
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 18 days ago by roy.granit800
0
votes
0
answers
158
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 20 days ago by roy.granit800
1
vote
1
answer
145
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 29 days ago by roy.granit800 • updated 29 days ago by grant.hovhannisyan1.8k
0
votes
2
answers
136
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 5 weeks ago by roy.granit800
0
votes
2
answers
136
views
2
answers
Comment: C: How does one count unmapped transcripts ?
... After adaptor cleaning I have about 30% of unaligned reads therefore I wish to inspect these reads and see what is the source, ideally it would be great to blast these sequences since I have no clue if these originate due to bacterial or viral contamination. ...
written 5 weeks ago by roy.granit800
0
votes
2
answers
136
views
2
answers
Comment: C: How does one count unmapped transcripts ?
... But how do I find the most common reads to blast them? ...
written 5 weeks ago by roy.granit800
0
votes
2
answers
136
views
2
answers
Comment: C: How does one count unmapped transcripts ?
... Indeed, I'm aware that I cannot align these sequences to the transcriptome/genome, but these reads are derived from a certain cell line which might express some 'external' genes that were transfected and I wish to know how many of the reads map to these genes (before I generate a hybrid genome) ...
written 5 weeks ago by roy.granit800
0
votes
0
answers
131
views
0
answers
Comment: C: Plotting CNV matrix as heatmap using python
... Ended using https://github.com/broadinstitute/infercnv which runs from R but has great functionality ...
written 5 weeks ago by roy.granit800
8
votes
2
answers
136
views
6 follow
2
answers
How does one count unmapped transcripts ?
... Hello all, I have a list of un-mapped reads, is there a way to generate a ranked list of transcripts, meaning count the most frequent ones? Thanks! ...
rna-seq written 5 weeks ago by roy.granit800 • updated 5 weeks ago by Charles Warden7.3k
1
vote
0
answers
131
views
0
answers
Plotting CNV matrix as heatmap using python
... I have a marix with chromosome location and copy number data which looks like this chr start cell_1 cell_2 cell_3 1 9997206 1.42 -0.25 -0.84 1 9997306 -0.47 -0.32 -0.34 1 9997406 -0.51 0.19 -2.06 1 9997506 0.23 -0.2 0.27 1 9997606 -0.41 -0.27 -2.02 I wish to plot this data ...
python cnv heatmap written 10 weeks ago by roy.granit800

Latest awards to roy.granit

Great Question 7 months ago, created a question with more than 5,000 views. For What is the input for clusterProfiler R pack
Popular Question 7 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 8 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Centurion 15 months ago, created 100 posts.
Popular Question 16 months ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: About gene id
Supporter 20 months ago, voted at least 25 times.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: About gene id
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to import a big matrix into matlab?
Scholar 4.4 years ago, created an answer that has been accepted. For A: Genes and respective pathways from FTP database
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: About gene id
Autobiographer 4.4 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: 3191 users visited in the last hour