User: Mathew Bunj

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Mathew Bunj40
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7 years ago
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Posts by Mathew Bunj

<prev • 12 results • page 1 of 2 • next >
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Question about comparing expression in different data
... I have 4 datasets of gene expression from different organisms that I want to compare. For PCA comparison will it be reasonable to take genes present in all datasets, so as to avoid biases (easy interprettaion) if the gene is present in one dataset or two datasets ...
rnaseq expression written 21 days ago by Mathew Bunj40
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Comment: C: Question About Vcf4.1 File
... Thanks, that is helpful. Is there a documentation which I may keep on referring in future. ...
written 6.1 years ago by Mathew Bunj40
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Question About Vcf4.1 File
... I have a VCF version 4.1 which has CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Normal Tumor 1 11049 . G . . . NS=2;AN=2 GT:PS 0/0:. ./.:. Where can I find the meaning of these 0/0:. ./.:. I read http://www.1000genomes.or ...
vcf file written 6.1 years ago by Mathew Bunj40 • updated 4.3 years ago by cpad011212k
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Is Gatk Available Via The In Genepattern Software?
... I thoroughly looked at http://genepattern.broadinstitute.org/gp/pages/index.jsf but could not find GATK pipeline under broad's public analysis pipelines. Am I missing something or it has not been added under gene pattern? Thanks ...
gene gatk written 6.4 years ago by Mathew Bunj40 • updated 6.4 years ago by Istvan Albert ♦♦ 82k
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Answer: A: Rna-Seq Analysis With Bacteria, Rrna Reduced, Strand Specific
... Bowtie 2 should be fine, I dont think you need TopHat2, BTW what was the purpose of Ribo zero library? ...
written 6.8 years ago by Mathew Bunj40
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Shrimp2 For Rna-Seq
... I was wondering if I can use SHRIMP2 for RNA-seq alignments of a viral genome? I have not see any paper on this and wonder if I am thinking it rightly or it is mainly used in DNA seq variation analysis? ...
alignment rna-seq written 6.9 years ago by Mathew Bunj40 • updated 6.9 years ago by JC9.3k
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Comment: C: Which Parameter To Select -P (Pe Mode) In Shrimp2
... Could you be little more specific. ...
written 7.0 years ago by Mathew Bunj40
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Comment: C: Aligning Miseq With Deletions >10 Bases
... I will be curious to see how BWA works on such long reads. ...
written 7.0 years ago by Mathew Bunj40
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Comment: C: Which Aligner Is Best Suited For Clip-Seq Data?
... The procedure include UV cross link and yes it may be possible it can generate soem mutations particularly T to C. Do You have any suggestion? ...
written 7.0 years ago by Mathew Bunj40
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Which Aligner Is Best Suited For Clip-Seq Data?
... I have an RNAseq data (CLIP-seq) and want to find out RNA-binding partner to my proteins of interest. The data is PE 2X50. Which aligner will be most suitable to detect RNAs in my sequencing data? Thanks. ...
alignment rna sequencing written 7.0 years ago by Mathew Bunj40 • updated 7.0 years ago by 141341254653464453.5k

Latest awards to Mathew Bunj

Great Question 6.1 years ago, created a question with more than 5,000 views. For Which Aligner Is Best Suited For Clip-Seq Data?
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Which Aligner Is Best Suited For Clip-Seq Data?
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Is Gatk Available Via The In Genepattern Software?
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Shrimp2 For Rna-Seq
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Question About Vcf4.1 File
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Bacterial Rna-Seq

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