User: Michi

gravatar for Michi
Michi930
Reputation:
930
Status:
Trusted
Location:
Barcelona
Website:
http://bg.upf.edu/
Last seen:
1 day, 10 hours ago
Joined:
3 years, 10 months ago
Email:
m******************@gmail.com

Posts by Michi

<prev • 96 results • page 1 of 10 • next >
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Comment: C: Extracting Reads Containing A Specific Variant From A Bam File
... lovely solution! I wanted to filter the read pairs also, in which case I used your command to get the read names, stored them in an intermediate file and then extracted the same info (using fillmd) to get the read pairs into a .sam file ...
written 4 days ago by Michi930
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Answer: A: Iterating through paired-end reads in samtools / pysam
... I agree that it should be a bit simpler, given that paired end bam files are so common. I used the following solution, which is only applicable if the .bam file has been previously sorted by read names `samtools sort -n`! samfile = AlignmentFile(filename, 'rb') # BAM file reader. # It ...
written 4 weeks ago by Michi930
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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 3 months ago by Michi930 • updated 3 months ago by Ram16k
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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 Unluckily the example code link is no longer valid.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 3 months ago by Michi930
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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 3 months ago by Michi930
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Comment: C: Custom genome and tophat
... It seems that this did the trick. ...
written 19 months ago by Michi930
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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 19 months ago by Michi930
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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 19 months ago by Michi930
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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 19 months ago by Michi930
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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 22 months ago by Michi930

Latest awards to Michi

Popular Question 3 months ago, created a question with more than 1,000 views. For How to annotate your vcf files with the GT (genotype) field
Student 5 months ago, asked a question with at least 3 up-votes. For Check Ancestry Relation Between Go Terms
Popular Question 15 months ago, created a question with more than 1,000 views. For Mpileup BCF/VCF output without non-ref base 'X'?
Popular Question 15 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 18 months ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 22 months ago, created a post with more than 5 votes. For A: Please Show Me To Solve Import Problem Of Gitools
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 22 months ago, created a question with more than 1,000 views. For Check Ancestry Relation Between Go Terms
Guru 22 months ago, received more than 100 upvotes.
Popular Question 2.4 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 2.5 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 2.7 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 2.8 years ago, created an answer that has been accepted. For A: Mpileup BCF/VCF output without non-ref base 'X'?
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Appreciated 3.6 years ago, created a post with more than 5 votes. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
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Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: What Is The Best Method To Find Orthologous Genes Of A Species?
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Good Answer 3.6 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 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Master'S In Bioinformatics

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