User: Michi

gravatar for Michi
Michi900
Reputation:
900
Status:
Trusted
Location:
Barcelona
Website:
http://bg.upf.edu/
Last seen:
1 month ago
Joined:
3 years, 4 months ago
Email:
m******************@gmail.com

Posts by Michi

<prev • 91 results • page 1 of 10 • next >
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Comment: C: Custom genome and tophat
... It seems that this did the trick. ...
written 13 months ago by Michi900
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Comment: C: Custom genome and tophat
... That makes sense! Altough a pity since I don't like to 'alter' the genomic position. I'll give it a try - thank you ...
written 13 months ago by Michi900
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Custom genome and tophat
... Hi I am creating a custom genome since I want to detect two genes only in my rna-seq reads. I have created a .fa as well as a gtf file - both extracts of the original genome.fa and the original gtf. My genome-fasta and gtf contain the two regions of interest. The header of the .fa file clearly st ...
tophat rna-seq sequencing written 13 months ago by Michi900
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Single Gene-Fusion detection - resource effective approaches?
... Hi I have a series of RNA-samples and we are interested in detecting one particular gene-fusion only. What would be a time-effective solution? Do you know of an existing fusion-tool which accepts regions of interest in order to not align to the whole genome? Thanks for your opinions and suggest ...
gene-fusion alignment rna-seq sequencing written 13 months ago by Michi900
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Answer: A: R -- Get Exonic Ranges Of A Gene'S Transcripts Given Its Name?
... Lets get the exons for the PLEC gene in HG19: http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=5339 library("GenomicFeatures") library("TxDb.Hsapiens.UCSC.hg19.knownGene") genome <- TxDb.Hsapiens.UCSC.hg19.knownGene # the plec gene plec_ge ...
written 16 months ago by Michi900
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Comment: C: How to annotate your vcf files with the GT (genotype) field
... Thanks! In any case - given that samtools does not do it (fixed in r880+ says it should) - do you know any other way of annotating the .vcf file with the GT field..? ...
written 20 months ago by Michi900
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Comment: C: How to annotate your vcf files with the GT (genotype) field
... Hi - I have edited my post and put the exact command ;) ...
written 20 months ago by Michi900
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Comment: C: Tools to view fastq file
... Hi: fastq files are normally just sequences without the information where in the genome they align - so IGV and other genome browsers cannot really reperesent it accurately ...
written 20 months ago by Michi900
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How to annotate your vcf files with the GT (genotype) field
... Hi there So I am generating a .vcf file with `samtools mpileup` which is piped through `bcftools view` and `bcftools norm`. In the output I kindly get the fields `DP` and `AD` amongst others for which I asked for in the `mpileup` options. What I am not getting is the `GT` field and neither the docu ...
vcf samtools genotype mpileup sequencing written 20 months ago by Michi900
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Comment: C: How To Sort Bed Format File
... what a nice side-effect ...
written 21 months ago by Michi900

Latest awards to Michi

Popular Question 9 months ago, created a question with more than 1,000 views. For Mpileup BCF/VCF output without non-ref base 'X'?
Popular Question 9 months ago, created a question with more than 1,000 views. For Alignment plot of a small extract (sequence) from a .bam file
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Please Show Me To Solve Import Problem Of Gitools
Popular Question 16 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Popular Question 16 months ago, created a question with more than 1,000 views. For Check Ancestry Relation Between Go Terms
Guru 16 months ago, received more than 100 upvotes.
Popular Question 22 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Popular Question 23 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Mpileup BCF/VCF output without non-ref base 'X'?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Should Biostar Be Switched Over To The Stackexchange Network?
Voter 2.5 years ago, voted more than 100 times.
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
Good Question 3.1 years ago, asked a question that was upvoted at least 5 times. For Check Ancestry Relation Between Go Terms
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Master'S In Bioinformatics
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Please Show Me To Solve Import Problem Of Gitools
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Master'S In Bioinformatics
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Check Ancestry Relation Between Go Terms
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Call Loss / Gain On Cgh Data When Tumor And Normal Are Not Analysed Together?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For 53893 Genes In Ensembl?

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