User: Jordan

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Jordan1.0k
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Posts by Jordan

<prev • 171 results • page 1 of 18 • next >
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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 2.3 years ago by Jordan1.0k
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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 2.4 years ago by Jordan1.0k
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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 2.4 years ago by Jordan1.0k
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Comment: C: TCGA normalized count data of 1000 samples for DGE
... If you have count data, you could try edgeR. ...
written 2.4 years ago by Jordan1.0k
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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 2.5 years ago by Jordan1.0k
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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 2.8 years ago by Jordan1.0k
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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 2.8 years ago by Jordan1.0k • updated 2.8 years ago by Ying W3.6k
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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 2.8 years ago by Jordan1.0k
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Proper regex to mark duplicates using Picard tools on SOLiD data
... Hi, I'm having trouble removing duplicates using Picard tools on SOLiD data. I get a regex not matching error. The reads have the following names: 22_758_632_F3 604_1497_576 124_1189_1519_F5 358_1875_702_F5-DNA And I don't think Picard tools is able to pick these read names with its default ...
bams duplicate-removal picard-tools solid ngs written 2.8 years ago by Jordan1.0k
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Comment: C: Mark Duplicates from Picard does not seem to recognize my sorted BAM files.
... I did get it fixed. What kind of error do you get? ...
written 2.8 years ago by Jordan1.0k

Latest awards to Jordan

Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Sequence Length Distribution From A Fastq File
Scholar 9 months ago, created an answer that has been accepted. For A: Need help using Shrimp2 on paired end SOLiD data.
Popular Question 9 months ago, created a question with more than 1,000 views. For How To Identify Large Arrangements And Transposable Elements In Ngs Data?
Student 9 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 9 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 9 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 9 months ago, created a question with more than 1,000 views. For Need help understanding read depth for somaticsniper vcf's
Epic Question 10 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 11 months ago, created a question with more than 1,000 views. For Where Can I Download Ws182 Genome Of C. Elegans?
Popular Question 15 months ago, created a question with more than 1,000 views. For What Do Marked Reads Mean In An Xsq File?
Popular Question 15 months ago, created a question with more than 1,000 views. For Is There A Way To Download The Human Exome?
Popular Question 15 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?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Different Types Of Genes
Popular Question 15 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 15 months ago, created a question with more than 1,000 views. For Variant callers for Ion Torrent data?
Popular Question 15 months ago, created a question with more than 1,000 views. For Where Can I Download Ws182 Genome Of C. Elegans?
Popular Question 18 months 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 18 months ago, created a question with more than 1,000 views. For Is There A Way To Download The Human Exome?
Guru 18 months ago, received more than 100 upvotes.
Popular Question 18 months 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 19 months ago, created a question with more than 1,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Popular Question 21 months ago, created a question with more than 1,000 views. For Is There A Way To Download The Human Exome?
Popular Question 21 months ago, created a question with more than 1,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Great Question 23 months ago, created a question with more than 5,000 views. For How Can I Know The Length Of Mapped Reads From Bam File?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Coursera: Computational Molecular Evolution

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