User: dganiewich

gravatar for dganiewich
dganiewich120
Reputation:
120
Status:
Trusted
Location:
Buenos Aires, Argentina
Last seen:
3 days, 7 hours ago
Joined:
1 year, 10 months ago
Email:
d*********@leloir.org.ar

Posts by dganiewich

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to obtain a segmentation file from Control-FREEC output to use with GISTIC
... Gracias Kevin!! I will try and generate the bed and do the overlap with *GenomicRanges* (and will definitely put the code here if I succeed). I didn't like the idea of using *DNAcopy* as for what I have read, specificity is very low for Exome data, unlike Control-FREEC which is more reliable. Anywa ...
written 8 months ago by dganiewich120
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How to obtain a segmentation file from Control-FREEC output to use with GISTIC
... Hello everyone, I would like to perform a GISTIC analysis on a set of WES samples which I have analyzed with Control-FREEC. This program does not output the regular segmentation file with ID, Chrom, Start, End, num markers, log ratio which is needed for GISTIC, neither does it output the markers ...
gistic control-freec written 8 months ago by dganiewich120 • updated 8 months ago by Kevin Blighe67k
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Update below, even Batch Effect removal was not enough ...
written 15 months ago by dganiewich120
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Answer: A: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... For anyone that encounters a similar situation: Even after batch effect removal, the library method is so different that it was not possible to compare them after all. QC plots showed that samples still clustered by library method and separated from their own same origin sample. This paper helped ...
written 15 months ago by dganiewich120
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Thank you for your comment skbrimer! ...
written 16 months ago by dganiewich120
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Great point. It is indeed for mRNA. Thanks ...
written 16 months ago by dganiewich120
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Comment: C: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
... Thank you kristoffer! I will definitely use this! ...
written 16 months ago by dganiewich120
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Can I perform differential gene expression with samples from Poly-A and Ribo-deplation ?
... Hi, I have a question regarding differential gene expression analysis when the samples library method is different. I have 10 samples total, 3 from one condition and 7 from the other. Among the first 3, 2 where sequenced using poly-a and one with ribo depletion library preparation method. In the ...
rna-seq differential expression written 16 months ago by dganiewich120
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Comment: C: CWL docker command user
... I just realized that you use the Github file and not the Docker image, maybe that is what I am doing wrong... I'll check and get back to you ! ...
written 17 months ago by dganiewich120
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Comment: C: CWL docker command user
... Hi Tom, thank you very much for your help! Indeed, I have stuggled a lot with bioinformatic stuff !! I'm sorry for my belated response, but I have yet not been able to make it work... Maybe there is something wrong with my importation of the dockerfile? Just to be sure, my new code has: #!/us ...
written 17 months ago by dganiewich120

Latest awards to dganiewich

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I perform differential gene expression with samples from Poly-A and Ribo-dep
Popular Question 7 months ago, created a question with more than 1,000 views. For GATK4 Mutect2 variants IDs not shown
Scholar 18 months ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown
Scholar 20 months ago, created an answer that has been accepted. For A: GATK4 Mutect2 variants IDs not shown

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