User: Jordan

gravatar for Jordan
Jordan1.1k
Reputation:
1,150
Status:
Trusted
Location:
Pittsburgh
Scholar ID:
Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
7 years, 6 months ago
Email:
a******@gmail.com

about me

Posts by Jordan

<prev • 183 results • page 1 of 19 • next >
0
votes
0
answers
107
views
0
answers
Error while running vcf2maf tool
... Hi, I'm running vcf2maf.pl on about 100 VCF files. But some files (about 10) do not report any MAF, and they report the below error: Can't exec "/bin/sh": Argument list too long at /home/.conda/envs/variant_calling/bin/vcf2maf.pl line 376. Use of uninitialized value in concatenation (.) or ...
variant-calling maf vep vcf2maf vcfs written 10 weeks ago by Jordan1.1k
1
vote
1
answer
179
views
1
answers
Comment: C: How do you know the best segments in cnvkit after filtering?
... Thank you! Looking at the weight and CN values looks like the best way to go. ...
written 3 months ago by Jordan1.1k
2
votes
1
answer
179
views
1
answer
How do you know the best segments in cnvkit after filtering?
... Hi, I'm working on WGS data using cnvkit. I filtered the segments using `segmetrics` and `call`. Here are my steps: cnvkit.py segmetrics tumor.cnr -s tumor.cns --ci --sem -o tumor.segmetrics.cns cnvkitpy call tumor.segmetrics.cns --filter ci -o tumor.segmetrics.call.cns I have about 300 s ...
cnvkit cnv wgs written 4 months ago by Jordan1.1k • updated 4 months ago by brunobsouzaa230
0
votes
1
answer
209
views
1
answers
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 4 months ago by Jordan1.1k
0
votes
1
answer
209
views
1
answers
Comment: C: The center in scatter plot generated by CNVkit looks off
... These are female samples. ...
written 4 months ago by Jordan1.1k
0
votes
0
answers
240
views
0
answers
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 4 months ago by Jordan1.1k
1
vote
0
answers
240
views
0
answers
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 4 months ago by Jordan1.1k
0
votes
1
answer
209
views
1
answer
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 4 months ago by Jordan1.1k • updated 4 months ago by d-cameron2.2k
2
votes
1
answer
236
views
1
answer
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 9 months ago by Jordan1.1k • updated 8 months ago by Kevin Blighe63k
0
votes
0
answers
338
views
0
answers
(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 2.0 years ago by Jordan1.1k

Latest awards to Jordan

Student 6 months 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 8 months ago, created a question with more than 5,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Great Question 12 months ago, created a question with more than 5,000 views. For Variant callers for Ion Torrent data?
Great Question 12 months ago, created a question with more than 5,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Great Question 12 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 17 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 17 months ago, voted more than 100 times.
Great Question 24 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 24 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 2.5 years ago, created a question with more than 5,000 views. For Variant callers for Ion Torrent data?
Student 2.5 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 2.5 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 2.5 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 2.5 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 3.1 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 3.1 years ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Student 3.7 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 3.7 years ago, created an answer that has been accepted. For A: Need help using Shrimp2 on paired end SOLiD data.
Popular Question 3.7 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 3.7 years ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 3.7 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 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Sequence Length Distribution From A Fastq File

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1551 users visited in the last hour