User: roy.granit
roy.granit • 830
- Reputation:
- 830
- Status:
- Trusted
- Location:
- Israel/LabWorm
- Website:
- http://roygranit.me/
- Twitter:
- rgranit
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 weeks, 3 days ago
- Joined:
- 5 years, 11 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, how reliable is bbmap? never heard of it.. ...
written 9 weeks ago by
roy.granit • 830
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... I did not mention that some of these genes do not exist in the genome.. ...
written 9 weeks ago by
roy.granit • 830
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... I have 3 amplicons that I have sequenced and now I wish to align them to the sequences of these three genes so I can quantify how many reads mapped to each gene.
In order to use STAR must I go through the steps of genome indexing or is there a way to align stright with the fasta file containing the ...
written 9 weeks ago by
roy.granit • 830
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... I have a human DNA sequence and I wish to check how variable this sequence is.. is there a way to check how many SNPs are found at the given location?
Thanks! ...
written 11 weeks ago by
roy.granit • 830
• updated
11 weeks ago by
Pierre Lindenbaum ♦ 129k
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... I wish to know if the overlap of ALL three lists together is significant, so I don't believe that contingency table would fit this use case. ...
written 3 months ago by
roy.granit • 830
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... Hi All,
I have 3 independent lists of genes, and I would like to assess the statistical significance of the intersection of the lists. For two groups I have used hypergeometric test, but I'm uncertain what should be done here.
Any ideas?
Thanks! ...
written 3 months ago by
roy.granit • 830
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Comment:
C: ChIP to genes
... I found these tools: http://bioconductor.org/packages/devel/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html and http://great.stanford.edu/public/html/ ...
written 3 months ago by
roy.granit • 830
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... Hi All,
I have ChIP seq in the form of peaks per region:
chr start end abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue)
chr1 856361 856664 856411 21 8.69656 4.06641 5.75518
chr1 859109 859948 859481 50 35.20025 9.42667 31.0408
chr1 877214 877610 877418 20 7.99405 3.8 ...
written 3 months ago by
roy.granit • 830
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... Thanks, it ran OK with just `cutadapt` ...
written 5 months ago by
roy.granit • 830
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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 5 months ago by
roy.granit • 830
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