User: mhasa006

gravatar for mhasa006
mhasa00610
Reputation:
10
Status:
New User
Location:
United States
Last seen:
2 days, 14 hours ago
Joined:
2 years, 5 months ago
Email:
m*******@ucr.edu

Posts by mhasa006

<prev • 14 results • page 1 of 2 • next >
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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 7 days ago by mhasa00610
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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 22 days ago by mhasa00610
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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 24 days ago by mhasa00610 • updated 24 days ago by Jacob Warner490
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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 4 weeks ago by mhasa00610
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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 4 weeks ago by mhasa00610 • updated 4 weeks ago by Kevin Blighe3.2k
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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 15 months ago by mhasa00610
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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 23 months ago by mhasa00610
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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 23 months ago by mhasa00610
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Comment: C: Nucleosome positioning dataset
... Thanks, Where can I find nucleosome positioning dataset of C.alegra? ...
written 2.2 years ago by mhasa00610
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Nucleosome positioning dataset
... Could anyone help me find publicly available nucleosome positioning datasets? ...
dataset nucleosome nucleosome positioning written 2.2 years ago by mhasa00610 • updated 10 weeks ago by chrisclarkson10050

Latest awards to mhasa006

Popular Question 15 months ago, created a question with more than 1,000 views. For Pulse information of PacBio data
Popular Question 15 months ago, created a question with more than 1,000 views. For PacBio data assembly with Celera

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