User: Jordan

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Jordan1.1k
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Posts by Jordan

<prev • 180 results • page 1 of 18 • next >
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Comment: C: The center in scatter plot generated by CNVkit looks off
... All the samples are female. I was a bit worried to see Y chromosome having so many deletions even if both normals and tumors are female samples. Other papers I have seen do not have such high deletions in the Y chromosomes as well. ...
written 20 hours ago by Jordan1.1k
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Comment: C: The center in scatter plot generated by CNVkit looks off
... These are female samples. ...
written 2 days ago by Jordan1.1k
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Comment: C: How are the log2 values in CNVkit .cnr files calculated?
... I read that part of the manual, but I’m still not clear about it. If I’m understanding that document correctly, weights are used for log2 ratio calculation? ...
written 7 days ago by Jordan1.1k
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How are the log2 values in CNVkit .cnr files calculated?
... Hi, I'm relatively new to CNV analysis. I ran cnvkit on WGS samples (4 tumor/normals) and the normals were pooled. I don't quite understand how the log2 values in .cnr files for CNVkit are calculated. Here is a result from one of my sample: normal.cnn: chr1 11129 12259 DDX11L1 28.2027 4.81772 ...
cnvkit .cnr cnv wgs written 7 days ago by Jordan1.1k
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The center in scatter plot generated by CNVkit looks off
... Hi, I ran CNVkit piplene on WGS samples. I have 4 tumor/normals and pooled the normals. Here is the command I used: ` cnvkit.py batch -p $OMP_NUM_THREADS $BAMs/*_T*.bam -n $BAMs/*_B*.bam -m wgs -f $refs --annotate $refFlat --output-reference $out/project.cnn --output-dir $out ` I dropped low ...
scatter-plot cnvkit wgs written 7 days ago by Jordan1.1k • updated 20 hours ago by d-cameron2.1k
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Creating a panel of normal from one normal sample
... Hi, I have just one normal sample and 3 tumors from the same patient. In this case is it ok to generate PoN using the following code? gatk --java-options "-Xmx16g" Mutect2 \ -R $ref \ -I $BAMs/normal.bam \ -tumor normal \ --germline-resource somatic-hg38-af-only ...
variant-calling gatk mutect2 panelofnormals written 4 months ago by Jordan1.1k • updated 4 months ago by Kevin Blighe56k
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(Closed) Time take for protein protein interaction validation methods
... Hi, Is there a way to know how much time it takes to conduct a protein protein interaction experiment? I'm looking for overall experiment time for techniques like: 1. Tandem affinity purification-mass spectroscopy (TAP-MS) 2. Coimmunoprecipitation 3. Protein microarrays 4. Phage display 5. X-ray c ...
y2h assays proteins interactome written 20 months ago by Jordan1.1k
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Comment: C: Tools for asserting matching pairs of samples from the same patient
... That's the kind of tool I was looking for. Thanks! ...
written 2.2 years ago by Jordan1.1k
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Tools for asserting matching pairs of samples from the same patient
... In a RNA-Seq project, I have 10 samples, 2 each from 5 patients. I would like to make sure the patients or sample pairs were labeled properly and that there was no mix up. I used the counts from HT-Seq to generate MDS and scatter plots to assess them. The plots suggest, there might be a mix up. Bu ...
ngs rna-seq written 2.2 years ago by Jordan1.1k • updated 2.2 years ago by dariober11k
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Comment: C: Add read group to header after samtools merge
... Did you find a solution for this? I'm having the same issue. ...
written 4.9 years ago by Jordan1.1k

Latest awards to Jordan

Student 10 weeks ago, asked a question with at least 3 up-votes. For How To Deal With Technical And Biological Replicates With Tophat2 For Rna-Seq Data
Great Question 4 months ago, created a question with more than 5,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
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Great Question 8 months ago, created a question with more than 5,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Extract Regions From A Bam To A Bed File Where The Average Mapping Quality Is Be
Voter 13 months ago, voted more than 100 times.
Great Question 19 months ago, created a question with more than 5,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Popular Question 19 months ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Great Question 2.1 years ago, created a question with more than 5,000 views. For Variant callers for Ion Torrent data?
Student 2.1 years ago, asked a question with at least 3 up-votes. For How Can I Know The Length Of Mapped Reads From Bam File?
Great Question 2.1 years ago, created a question with more than 5,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Student 3.4 years ago, asked a question with at least 3 up-votes. For Help With Understanding Macs Output. What Does Tags And Summit Exactly Mean?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Need help using Shrimp2 on paired end SOLiD data.
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How To Identify Large Arrangements And Transposable Elements In Ngs Data?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Sequence Length Distribution From A Fastq File

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