User: Michi

gravatar for Michi
Michi910
Reputation:
910
Status:
Trusted
Location:
Barcelona
Website:
http://bg.upf.edu/
Last seen:
1 week, 2 days ago
Joined:
3 years, 7 months ago
Email:
m******************@gmail.com

Posts by Michi

<prev • 94 results • page 1 of 10 • next >
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Comment: C: Sorting bed files with bash sort
... -k1,1V -k2,2g Add semantic version sort to the first key for the chromosomes to be sorted correctly. ...
written 15 days ago by Michi910 • updated 15 days ago by Ram14k
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Comment: C: General questions about running GSEAPreranked
... Unluckily the example code link is no longer valid. Do you know where it has moved or do you have a copy of your own? ...
written 22 days ago by Michi910
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Answer: A: How to find out the insert size in RNA seq data
... also `samtools` has a very similar command to `bamtools`: `samtools stats --insert-size foo.bam` you can additionally speed upt the process by using `--threads 10` ...
written 25 days ago by Michi910
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Comment: C: Custom genome and tophat
... It seems that this did the trick. ...
written 16 months ago by Michi910
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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 16 months ago by Michi910
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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 16 months ago by Michi910
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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 16 months ago by Michi910
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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 19 months ago by Michi910
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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 23 months ago by Michi910
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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 23 months ago by Michi910

Latest awards to Michi

Popular Question 22 days ago, created a question with more than 1,000 views. For How to annotate your vcf files with the GT (genotype) field
Student 11 weeks ago, asked a question with at least 3 up-votes. For Check Ancestry Relation Between Go Terms
Popular Question 12 months ago, created a question with more than 1,000 views. For Mpileup BCF/VCF output without non-ref base 'X'?
Popular Question 12 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 15 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Please Show Me To Solve Import Problem Of Gitools
Popular Question 19 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 19 months ago, created a question with more than 1,000 views. For Check Ancestry Relation Between Go Terms
Guru 19 months ago, received more than 100 upvotes.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 2.4 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 2.5 years ago, created an answer that has been accepted. For A: Mpileup BCF/VCF output without non-ref base 'X'?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Should Biostar Be Switched Over To The Stackexchange Network?
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Appreciated 3.3 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 3.3 years ago, asked a question that was upvoted at least 5 times. For Check Ancestry Relation Between Go Terms
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 3.4 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 3.4 years ago, created a post with more than 5 votes. For A: Master'S In Bioinformatics
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Please Show Me To Solve Import Problem Of Gitools
Good Answer 3.4 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 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Master'S In Bioinformatics
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Check Ancestry Relation Between Go Terms

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