User: roy.granit
roy.granit • 800
- Reputation:
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- Israel/LabWorm
- Website:
- https://labworm.com/
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- rgranit
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- Google Scholar Page
- Last seen:
- 2 weeks, 2 days ago
- Joined:
- 5 years, 1 month ago
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- 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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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.granit • 800
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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 20 days ago by
roy.granit • 800
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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 29 days ago by
roy.granit • 800
• updated
29 days ago by
grant.hovhannisyan • 1.8k
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... Thanks. Ended up using this code after converting my .mate1 files into bam using picardtools ...
written 5 weeks ago by
roy.granit • 800
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... 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.granit • 800
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... But how do I find the most common reads to blast them? ...
written 5 weeks ago by
roy.granit • 800
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... 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.granit • 800
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... Ended using https://github.com/broadinstitute/infercnv which runs from R but has great functionality ...
written 5 weeks ago by
roy.granit • 800
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6 follow
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... 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! ...
written 5 weeks ago by
roy.granit • 800
• updated
5 weeks ago by
Charles Warden ♦ 7.3k
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... 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 ...
written 10 weeks ago by
roy.granit • 800
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