User: Allpowerde

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Allpowerde1.2k
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Posts by Allpowerde

<prev • 47 results • page 1 of 5 • next >
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Pindel2Vcf: Reference Allele Length Issues
... It seems that for some variants (predominantly RPLs) pindel2vcf records the wrong END-value (which subsequently GATK complains about "ERROR MESSAGE: BUG: GenomeLoc 9:17427298-17427314 has a size == 18 but the variation reference allele has length 17") e.g. chr9 17427298 . TAGATTTTTC ...
vcf pindel written 3.8 years ago by Allpowerde1.2k • updated 3.1 years ago by Mitsuko.Korobkin0
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Answer: A: Pindel Segmentation Fault
... The reason for the segmentation fault seems to have something to do with the bam format produced by your aligner. My alignments are also created by an aligner other than BWA (in my case casava) and I do get the same segmentation fault even with the new version 0.2.5a3, Oct 24 2013 (Note, it is a new ...
written 3.8 years ago by Allpowerde1.2k
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Answer: A: The Impact Of Adenine-Rich Tracts On Pol Ii Pausing
... You could download publicly available RNAseq (whole RNA rather than Poly-A-tail filtered is more appropriate) data and have a look at the coverage at the transition from an A-rich region to regions with "normal" bp distribution. If there is pausing then I would expect more actively transcribed trans ...
written 4.9 years ago by Allpowerde1.2k
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New Tophat Adds Multimappers As Entirely New Reads
... What are the benefits/disadvantages of allowing multi-hits in tophat ? Since tophat2.0 the default mapping setting allows for multi-mappers or multi-hits. Documentation of Tophat 2.0.0 ... In addition to reporting the best (or primary) alignments (the original TopHat behavior), Top ...
tophat written 4.9 years ago by Allpowerde1.2k • updated 4.9 years ago by David Langenberger7.9k
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Answer: A: Vcf Format: Different Ways To Express The Same Variant Information
... Taking up this issue again: Is there a way to fix malformed vcf files (e.g. from complete genomics or illumina), which allow the reference to be empty for insertions. ...
written 6.0 years ago by Allpowerde1.2k
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Answer: A: Bio Research-Oriented Project Management Solutions?
... We are using redmine. It was originally developed for software engineering projects but is so flexible that it is pretty easy to add a bio-spin to it. E.g. Bugs can easily be extended to manage custom items, like a flowcell (with organism, sequencing type, samples,...). Redmine has an active communi ...
written 6.1 years ago by Allpowerde1.2k
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Answer: A: Hg19 Versus Grch37
... There are some differences here and there (e.g. "chr"-omitted and the annotations seems to be 0-indexed vs. 1-indexed) but nothing as drastic as you showed. It is still a major pain though. GATK has taken clear sides with making b37 their primary ref-genome but PLINK and GWAS study are hg19 based. ...
written 6.1 years ago by Allpowerde1.2k • updated 5.1 years ago by Jeremy Leipzig17k
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Identify Differentially Methylated Regions From Medip-Tiling-Array Data
... Has anyone had experience with MeDIP-type protocols and nimbelgen "Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter" array with the cy3 (green) channel containing input, and the cy5 (red) channel containing methyl-enriched DNA? I would like to identify the differentially methylated area ...
differential methylation microarray written 6.1 years ago by Allpowerde1.2k • updated 6.1 years ago by brentp22k
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Answer: A: Is There A Standard Format For Go Term Enrichment Results?
... I'm all for standards, but it probably goes as it always has: the (accidental) format of the most heavily used program is adopted as the standard. So why not contact the developers of these programs and get their opinion (and cooperation): GOMO AmiGO GONOME others ...
written 6.1 years ago by Allpowerde1.2k
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Answer: A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
... The Queensland Brain Institute is running a weekly Seminar Series with focus on the sequencing applications that are used within the Institute (e.g. Genome/Exome-sequencing, RNA sequencing, small RNA sequencing, Methylation analysis,...). All slides are available online and the material for the upco ...
written 6.1 years ago by Allpowerde1.2k

Latest awards to Allpowerde

Guru 3.6 years ago, received more than 100 upvotes.
Supporter 3.6 years ago, voted at least 25 times.
Good Answer 6.2 years ago, created an answer that was upvoted at least 5 times. For A: Casava 1.8 Vs Gatk
Good Question 6.3 years ago, asked a question that was upvoted at least 5 times. For How Important Is Bioinformatics And How To Make A Case For It?
Student 6.8 years ago, asked a question with at least 3 up-votes. For Merging Vcf Files And Filling In Missing Genotypes
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Merging Vcf Files And Filling In Missing Genotypes
Good Question 7.1 years ago, asked a question that was upvoted at least 5 times. For How To Determine If There Is A Cluster Of Reads Mapping To A Different Chromosome
Student 7.1 years ago, asked a question with at least 3 up-votes. For How To Determine If There Is A Cluster Of Reads Mapping To A Different Chromosome
Student 7.1 years ago, asked a question with at least 3 up-votes. For Summarizing Personal Genomics Data From A Large Number Of Individuals
Good Answer 7.2 years ago, created an answer that was upvoted at least 5 times. For A: Predicting Phenotype From Snp Data. Help!
Appreciated 7.2 years ago, created a post with more than 5 votes. For A: Predicting Phenotype From Snp Data. Help!
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Predicting Phenotype From Snp Data. Help!
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Ngs: How Many Reads Should Be Expected To Map To The Reference Sequence
Popular Question 7.4 years ago, created a question with more than 1,000 views. For What To Do With An Error In The Fastq Illumina Quality Scores
Good Answer 7.5 years ago, created an answer that was upvoted at least 5 times. For A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Appreciated 7.5 years ago, created a post with more than 5 votes. For A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Appropriate Podcasts For A Bioinformatician?
Good Question 7.5 years ago, asked a question that was upvoted at least 5 times. For Has Enhancer And Transcription Factor Binding Site Prediction Already Been Made Redundant?

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