User: frankie.north

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Posts by frankie.north

<prev • 6 results • page 1 of 1 • next >
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ANNOVAR Annotation VCF empty
... Hi all, I am trying to run ANNOVAR Annotation tool to remove known SNPs from my VCF file, however everytime I run ANNOVAR the table comes back empty? From what I can see there are no errors with my previous VCF file and it is aligned to hg19, therefore I do not know what I am doing wrong? This is ...
annovar vcf annotation rna-seq written 14 months ago by frankie.north10 • updated 14 months ago by Jennifer Hillman Jackson23k
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Answer: A: Collect Alignment Summary Metrics won't run?
... Thank you Jen, this worked! ...
written 14 months ago by frankie.north10
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Collect Alignment Summary Metrics won't run?
... Hi all, I am trying to run Collect Alignment Summary Metrics on my RNA Seq data and every time it keeps coming up with the error below. Prior to this I have aligned using BWA for Illumina and used the same reference genome which is UCSC Main hg19 imported into my history. Fatal error: Exit code 1 ...
alignmentsummary software error rna-seq written 14 months ago by frankie.north10
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Realigner Target Creator will not run?
... I have been running the pipeline below to try and call SNPs from RNA-Seq data but have encountered problems with Realigner Target Creator Tool in Galaxy. Can anyone see any obvious problems in the pipeline? Import ucsc.hg19.fasta, ucsc.hg19.dict, ucsc.hg19.fasta.fai, ucsc hg19 snps, 1000G indels a ...
sorting realignertargetcreator genome gatk snp written 15 months ago by frankie.north10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Comment: C: Too few reads after VarScan on RNA-Seq data?
... Thank you Jen, I shall try the troubleshooting tips you have suggested! ...
written 15 months ago by frankie.north10
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Too few reads after VarScan on RNA-Seq data?
... Hi all, I have been trying to initiate a protocol to call SNPs in RNA-Seq data, but have had a few problems. I have carried out the main steps below: Import known SNPs from hg19 and RNA-Seq data Convert to FASTQ FastQC on RNA-Seq data Convert to FastQSanger Split paired end reads into forwar ...
mpileup varscan snp tophat rna-seq written 15 months ago by frankie.north10 • updated 15 months ago by Jennifer Hillman Jackson23k

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