User: mhasa006

gravatar for mhasa006
mhasa00620
Reputation:
20
Status:
New User
Location:
United States
Last seen:
1 month ago
Joined:
2 years, 7 months ago
Email:
m*******@ucr.edu

Posts by mhasa006

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Cancer research for computer science student
... Thanks for the good wishes. And it's he :-) ...
written 4 weeks ago by mhasa00620
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Forum: Cancer research for computer science student
... Hello, I am a Ph.D. student in Computer Science. My research interest is in computational biology. I have finished a project on epigenetics and now I want to work on Cancer genetic. I am particularly interested in cancer research but I don't have much of an experience with it. My advisor does not wo ...
bioinformatics computer science forum research cancer written 5 weeks ago by mhasa00620 • updated 5 weeks ago by Michael Dondrup43k
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Comment: C: Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegic
... This is probably a very long shot to get an answer. Still, asking... Could you please describe how the "Estimated Background mutation frequencies per million bp" table in the supplementary document was calculated? Is it purely experimental? Is it possible to compute the table by us? @Bioinfosm ...
written 9 weeks ago by mhasa00620
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Comment: C: RSEM output file format
... Thank you very much! I apologize for not being clear enough about the question, but your answer actually answered my question. ...
written 11 weeks ago by mhasa00620
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RSEM output file format
... I followed the following tutorial for RNA-Seq data analysis. https://ycl6.gitbooks.io/rna-seq-data-analysis/ After performing the Differential expression analysis using R (https://ycl6.gitbooks.io/rna-seq-data-analysis/perform_de_analysis.html) the final output files are `DE_analysis.gene.txt` and ...
rsem rna-seq differential expression written 11 weeks ago by mhasa00620 • updated 11 weeks ago by Jacob Warner570
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Comment: C: Dataset preparation for driver/passenger gene discovery
... Thank you very much for your detailed reply. I'll read these links and ask a further question if any. ...
written 3 months ago by mhasa00620
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Dataset preparation for driver/passenger gene discovery
... I want to work on a project to find driver/passenger genes in cancer dataset. I want to build a statistical model by analyzing various types of data such as copy number variation, gene expression, methylation, somatic point mutations etc. on TCGA datasets like BRCA. Can someone explain the preproces ...
gene tcga snv snp cancer written 3 months ago by mhasa00620 • updated 3 months ago by Kevin Blighe9.3k
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Extract gff of a particular chromosome
... I have a gff file that contains all the information from Chromosome 1 - Chromosome 14. But I need gff information on individual chromosome basis. For example, I am performing some experiment on Chromosome 11 and trying to visualize my result on IGV. When I load the gff file in IGV it is showing gene ...
gff3 chromosome igv written 17 months ago by mhasa00620
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Comment: C: VCF file REF Column outputs all 'N'
... Thanks for the reply. here genome.fa is used for general purpose. I have the fasta file of the original genome. Is that what you meant? I also checked the positions in the original genome. There was no 'N' there. What could be the problem?  ...
written 2.1 years ago by mhasa00620
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VCF file REF Column outputs all 'N'
... I am doing SNP calling using samtools. The way I'm doing is following. - I had a .bam file that contains information for all chromosome together. - I extracted information for each chromosome and make separate bam file for each chromosome.  - I made a snpcall using mpileup. Separately each chromo ...
vcf snp written 2.1 years ago by mhasa00620

Latest awards to mhasa006

Popular Question 16 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 16 months ago, created a question with more than 1,000 views. For PacBio data assembly with Celera

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