User: Jordan

gravatar for Jordan
Jordan1.0k
Reputation:
1,030
Status:
Trusted
Location:
Pittsburgh
Scholar ID:
Google Scholar Page
Last seen:
3 months, 4 weeks ago
Joined:
5 years, 4 months ago
Email:
a******@gmail.com

about me

Posts by Jordan

<prev • 173 results • page 1 of 18 • next >
0
votes
2
answers
233
views
2
answers
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 5 months ago by Jordan1.0k
2
votes
2
answers
233
views
2
answers
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 5 months ago by Jordan1.0k • updated 5 months ago by dariober9.2k
0
votes
2
answers
6.7k
views
2
answers
Comment: C: Add read group to header after samtools merge
... Did you find a solution for this? I'm having the same issue. ...
written 3.0 years ago by Jordan1.0k
0
votes
1
answer
1.6k
views
1
answers
Answer: A: How to count novel and known splice junction reads from BAM
... I have never tried this. But may be you can use bamtobed tool to convert the regions in bam to bed format. And then find common regions between this bed file and the gtf file. You can may be try the following steps. Step1: Convert bam to bed bedtools bamtobed -i reads.bam > reads.bed Step2: C ...
written 3.1 years ago by Jordan1.0k
2
votes
4
answers
1.2k
views
4
answers
Answer: A: using cufflinks when investigating differential expression
... The tuxedo suite you have used does consider biological variability. And I don't think it's right to change methods just because you think there is biological variability. This biological variability might be true. Another problem might also be that, you are using only two replicates. Ideally you wo ...
written 3.1 years ago by Jordan1.0k
1
vote
0
answers
1.6k
views
0
answers
Comment: C: TCGA normalized count data of 1000 samples for DGE
... If you have count data, you could try edgeR. ...
written 3.1 years ago by Jordan1.0k
1
vote
2
answers
862
views
2
answers
Answer: A: Cufflinks 0.0.7 and CummeRbound
... I think galaxy has the latest cufflinks version (2.2.1). Look at the tool shed of cufflinks: https://toolshed.g2.bx.psu.edu/repository?repository_id=bd9dafa96fea7d66 The version 0.0.7 you mention is the galaxy tool version not the cufflinks version. ...
written 3.2 years ago by Jordan1.0k
0
votes
1
answer
2.0k
views
1
answers
Comment: C: NOT RESETTING NORMAL error using Varscan2
... I did what was suggested. I have a new problem now. There are no variants being generated. I used the following code: samtools mpileup -q 10 -f hg19.fasta -B normal.bam tumor.bam > normal-tumor.pileup java -XX:ParallelGCThreads=16 -Xmx16g -jar /usr/local/packages/VarScan/2.3.6/VarScan.jar som ...
written 3.5 years ago by Jordan1.0k
1
vote
1
answer
2.0k
views
1
answer
NOT RESETTING NORMAL error using Varscan2
... Hi, I'm running Varscan2 somatic caller for my analysis. I'm getting an error which I never received before. Not resetting normal file because chrM < chrY Not resetting normal file because chrM < chrY Not resetting normal file because chrM < chrY Not resetting normal file because chrM &l ...
variant-calling somatic varscan2 snp written 3.5 years ago by Jordan1.0k • updated 3.5 years ago by Ying W3.8k
1
vote
1
answer
1.4k
views
1
answers
Answer: A: Proper regex to mark duplicates using Picard tools on SOLiD data
... I was able to fix the issue, by adding -Xmx16g and increasing the RAM size. Apparently the RAM was not sufficient. ...
written 3.5 years ago by Jordan1.0k

Latest awards to Jordan

Popular Question 4 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 4 months ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Popular Question 11 months ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Popular Question 11 months ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Popular Question 11 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Sequence Length Distribution From A Fastq File
Student 18 months ago, asked a question with at least 3 up-votes. For Help With Understanding Macs Output. What Does Tags And Summit Exactly Mean?
Popular Question 18 months ago, created a question with more than 1,000 views. For Solid Sequencing Protocol And How To Obtain Quality Of Solid Reads?
Scholar 18 months ago, created an answer that has been accepted. For A: Need help using Shrimp2 on paired end SOLiD data.
Popular Question 18 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Identify Large Arrangements And Transposable Elements In Ngs Data?
Popular Question 18 months ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Epic Question 19 months ago, created a question with more than 10,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Popular Question 20 months ago, created a question with more than 1,000 views. For Where Can I Download Ws182 Genome Of C. Elegans?
Popular Question 24 months ago, created a question with more than 1,000 views. For How To Identify Large Arrangements And Transposable Elements In Ngs Data?
Popular Question 24 months ago, created a question with more than 1,000 views. For Where Can I Download Ws182 Genome Of C. Elegans?
Popular Question 24 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: Different Types Of Genes
Popular Question 24 months ago, created a question with more than 1,000 views. For What Do Marked Reads Mean In An Xsq File?
Popular Question 24 months ago, created a question with more than 1,000 views. For Can We Use Multiple Normal Bam Files As Input For Mutect To Generate Vcf Files?
Popular Question 24 months ago, created a question with more than 1,000 views. For Is There A Way To Download The Human Exome?
Guru 2.3 years ago, received more than 100 upvotes.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Is It Possible To Map Transcripts To Genes Given That We Have A .Gtf File?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For What Does Thickstart (Col 7) Or Thickend (Col 8) Mean In A Bed File?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Is There A Way To Download The Human Exome?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 914 users visited in the last hour