User: a11msp

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a11msp110
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European Union
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Posts by a11msp

<prev • 19 results • page 1 of 2 • next >
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Job: Postdoctoral Research Scientist at MRC LMS, London
... Postdoctoral positions are open in the newly established Functional Gene Control group at MRC London Institute for Medical Sciences (LMS) led by Dr Mikhail Spivakov (https://lms.mrc.ac.uk/research-group/functional-gene-control/). We combine experimental and computational approaches to study how geno ...
gene regulation job genomics written 8 days ago by a11msp110
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Comment: C: SNP calling on ChIP-seq data
... This task is daunting, but doable. The coverage at ChIP peaks for good datasets is actually quite reasonable.    I suggest you have a look at that paper. What they propose is still less robust than aligning to two haplotype-specific reference genomes and quantifying allelic imbalance directly. How ...
written 3.3 years ago by a11msp110
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Comment: C: SNP calling on ChIP-seq data
... First answer: to detect non-coding SNPs at regions that exome-seq does not enrich for. Second answer: to look for allelic imbalance in TF binding in the absence of per-haplotype reference genomes.   ...
written 3.3 years ago by a11msp110
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Comment: C: SNP calling on ChIP-seq data
... Thanks! I was inspired by this paper as well. Good point about allele-specific binding, which is why I focused only on those cases where the imbalance is in favour of the alternative allele.  ...
written 3.3 years ago by a11msp110
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SNP calling on ChIP-seq data
... I am trying to call SNPs from ChIP-seq data and currently, I'm using samtools mpileup for this. I am wondering however whether mpileup's SNP calling is affected by the assumption that we have individual-level genomic data and therefore all observed deviations in read count from the 1:1, or 0:1/1:0 r ...
ngs chip-seq snp written 3.3 years ago by a11msp110
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Comment: C: Affymetrix probeset IDs...
... Perfect, it worked, thanks so much! ...
written 4.0 years ago by a11msp110
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Comment: C: Affymetrix probeset IDs...
... Thanks a lot, will try this out tomorrow! ...
written 4.0 years ago by a11msp110
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Affymetrix probeset IDs...
... Hi everyone, I'm trying to look at the processed data for the following ArrayExpress entry: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-57818/ The array design for this experiment is specified as " [MoGene-2_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]". (Is it n ...
microarray affymetrix written 4.0 years ago by a11msp110 • updated 2.0 years ago by srinivasnvnk550
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Comment: C: Bwa Sampe Segmentation Fault
... Update: With this patch, the run lasted a little longer but eventually died in a very similar setting. Perhaps the patch is in the right place, but is not fully adequate... ...
written 6.0 years ago by a11msp110
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Comment: C: Bwa Sampe Segmentation Fault
... I posted this question to the bwa mailing list and received the following patch from Mark Kelly that may fix this bug: diff -crN bwa-0.6.1-orig/bwase.c bwa-0.6.1-fix/bwase.c *** bwa-0.6.1-orig/bwase.c Mon Nov 28 08:55:02 2011 --- bwa-0.6.1-fix/bwase.c Tue Jun 12 13:05:17 2012 *********** ...
written 6.0 years ago by a11msp110

Latest awards to a11msp

Great Question 3.0 years ago, created a question with more than 5,000 views. For Bwa Sampe Segmentation Fault
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Biopython Entrez.Efetch Problem
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Affymetrix probeset IDs...
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bwa Sampe Segmentation Fault
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Can Bcftools And Vaast Call Phased Genotypes?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Biopython Entrez.Efetch Problem
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Bwa Sampe Segmentation Fault

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