User: H.Hasani

gravatar for H.Hasani
H.Hasani640
Reputation:
640
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Trusted
Location:
Freiburg, Germany
Last seen:
1 day, 15 hours ago
Joined:
3 years, 2 months ago
Email:
h*************@yahoo.com

Posts by H.Hasani

<prev • 147 results • page 1 of 15 • next >
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Comment: C: Create snakefile based on R script
... I think you serisouly need to read & understand [snakemake tutorial][1] [1]: https://snakemake.readthedocs.io/en/stable/tutorial/basics.html ...
written 11 days ago by H.Hasani640
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Answer: A: Lolliplot graph for mutations
... in the site you mentioned there are number of things you need to understand correctly: - **snp**: this variable contatins contains the basic info of each mutation's position, e.g. in gene XXX on chr1:12345 - **sample.gr**: create a genomic interval object out of you list of mutations - **featur ...
written 8 weeks ago by H.Hasani640
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Answer: A: download tumor and normal data from TCGA
... The sample ID contains that information: the first 4 letters indicate project name, e.g. TCGA second two digits: tissue source third 4 digits: patient ID fifth 3 combinations: two digits representing sample type (1-9 tumor, 10-14 normal) my note on the previous answer is that the data I downloa ...
written 8 weeks ago by H.Hasani640
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How to get AF in TCGA MutSigNozzleReport2CV Level_4
... Dear all, after downloading TCGA-SNP level 4 from firehose; I noticed that the files have either all or some of the columns bellow. I'm wondering if they are indeed Allele Frequencies that were obtained from phase1 & 3 of 1000G project (as the name might reveal)? if that is the case then what a ...
tcga snp alele fraction written 8 weeks ago by H.Hasani640
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Answer: A: Bioinformatics terms that might be confusing for beginners
... Well, [Wikipedia][1] has a clear explanation for the Phred score! [1]: https://en.wikipedia.org/wiki/Phred_base_calling ...
written 3 months ago by H.Hasani640
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Comment: C: Interpretation of TCGA CNV data
... Hi, I used [Firehose][1] to download Gistic2 results. I have Level4 and the tables typically range between ` [-1.26300, 4.56500 ]`, I couldn't find any documentation explaining these numbers? i.e. I thought GISTIC ranges between -2 & 2? could you please help? [1]: http://firebrowse.org/ ...
written 5 months ago by H.Hasani640
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Comment: C: The outputs of GISTIC
... hi, were you able to find the answer to your question? ...
written 5 months ago by H.Hasani640
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Comment: C: error for barplot in enrichGO(clusterProfiler)
... I'm running into the same problem using simply `ggplot2` ... did you find a solution? ...
written 6 months ago by H.Hasani640
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Comment: C: Genotyping, genotype calling or SNP calling?
... Wouldn't you consider the notation given by current SNP callers [0/1,1/1,2/1...] as genotyping too? ...
written 6 months ago by H.Hasani640
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TCGA raw data (Level 1)
... Dear all, now that TCGA is closed, I was wondering if it is possible to obtain level 1 files. Those files were typically available via controled access. I tried [firehose][1] but I got only Level 3. I'm looking for SNP6 data (CEL files) and RNA (ideally fastq). In case not, could you please recomme ...
copy number rna-seq snp written 6 months ago by H.Hasani640

Latest awards to H.Hasani

Popular Question 3 months ago, created a question with more than 1,000 views. For csv into genome browser
Popular Question 7 months ago, created a question with more than 1,000 views. For How to Specify Genome Build in MutSigCV Input ?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to Specify Genome Build in MutSigCV Input ?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to Specify Genome Build in MutSigCV Input ?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to Specify Genome Build in MutSigCV Input ?
Scholar 19 months ago, created an answer that has been accepted. For A: csv into genome browser
Scholar 19 months ago, created an answer that has been accepted. For A: csv into genome browser
Commentator 22 months ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Centurion 2.3 years ago, created 100 posts.
Voter 2.6 years ago, voted more than 100 times.
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Supporter 3.0 years ago, voted at least 25 times.
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?
Scholar 3.2 years ago, created an answer that has been accepted. For A: How many SNPs are sufficiant for covering?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: How many SNPs are sufficiant for covering?

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