User: bioinforesearchquestions

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Posts by bioinforesearchquestions

<prev • 204 results • page 1 of 21 • next >
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Which one do I need to consider single-read or multi-read mappability bigwig file for creating mouse mappability file?
... Hi, I am using HMMcopy to generate copy number alterations for my samples. I am trying to create mm9 or mm10 mappability wiggle file from mouse bigwig file. I found the below mappability files from this article "Mappability of the mouse and human genomes and methylomes with Umap and Bismap" I a ...
mouse mm10 mm9 mappability hmmcopy written 17 hours ago by bioinforesearchquestions120
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Comment: C: How to create bigwig using mm10.fasta and mm10.fasta bowtie index files
... Hi Genomax, I reinstalled the tool it worked. ...
written 17 hours ago by bioinforesearchquestions120
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How to create bigwig using mm10.fasta and mm10.fasta bowtie index files
... Hi, I am trying to call copy number from mouse data using HMMcopy. Created the wig files for my BAM samples. Also created mm10_gc.wig using gcCounter (HMMcopy). I am facing issues while creating the big wig file. generateMap.pl -w 40 -i mm10 mm10.fa > mm10.bigwig Getting the following error ...
mouse wig bigwig hmmcopy written 1 day ago by bioinforesearchquestions120 • updated 1 day ago by ATPoint3.0k
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Comment: C: Need tools recommendation for plant RNAseq data
... Plant RNASeq data, paired-end, 101 bp from Illumina platform. ...
written 5 days ago by bioinforesearchquestions120
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Need tools recommendation for plant RNAseq data
... Hi, I have RNA data from 10 samples of Cannabis plant. I am planning to do the following analyses with these samples -) De novo Assembly (ex: Trinity, Velvet, SOAPdenovo, etc. Which is recommended for plants?) -) Variant calling ( does GATK support plant variant calling? -) Functional annotation ...
variant calling assembly plants rna-seq written 6 days ago by bioinforesearchquestions120 • updated 6 days ago by apeltzer90
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Is it possible to check whether a sample is progeny of the other two samples from exome sequenced data?
... Hi, I have exome sequenced reads from four samples. There is a sample mix-up. I have been asked to help on this issue. SampleA, SampleB, SampleC, SampleD What I really need to know is whether sampleA is the progeny of sampleB and sampleC? I generated the FASTQ files, BAM and variant calling file ...
exome ngs dna-seq snp written 13 days ago by bioinforesearchquestions120 • updated 13 days ago by Noushin N490
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Comment: C: How to validate the SNP calling pipeline?
... Thanks for the article and tools, Chen. I will read this paper and go over the tool for benchmarking. What are the standard strategies used to validate their variant calling pipeline? ...
written 13 days ago by bioinforesearchquestions120
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Comment: C: How to validate the SNP calling pipeline?
... Thanks for the article, Istvan. I will read this paper. ...
written 13 days ago by bioinforesearchquestions120
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Comment: C: How to validate the SNP calling pipeline?
... The main objective is to use the most widely-supported variant calling validation methodologies and build on them for the purpose of advanced annotation and phenotype interpretation. Trying to compile a list of metrics to validate. For example, I would like to look at SNP genotyping errors such as ...
written 13 days ago by bioinforesearchquestions120
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Comment: C: How to validate the SNP calling pipeline?
... Thanks, Pierre. I want to validate the called SNPs bioinformatically not via sanger sequencing. ...
written 13 days ago by bioinforesearchquestions120

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