User: kjb322

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kjb32210
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Posts by kjb322

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Answer: A: MPileup calling every base as <X>
... I have re run the workflow to correct the odd inputs you mentioned but found the same issue. Acutally, by filtering the output vcf from MPileup I found that the variants are and so it appears that it is ANNOVAR that I am having trouble with. Even with a filtered vcf containing only variants, ANNOVAR ...
written 22 months ago by kjb32210
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Comment: C: MPileup calling every base as <X>
... It's fine, its public data anyway! Any help at all by Monday would be greatly appreciated if possible and thanks again either way.   P.s. In order to not interfere wth that history, is it possible for me to use the uploaded data is this history from another? ...
written 22 months ago by kjb32210
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Comment: C: MPileup calling every base as <X>
... The history has got pretty messy as I have been trying everything the firstly identify the point where it goes wrong and then to try and solve it. https://usegalaxy.org/u/kelly-hunter/h/galaxy-presentation Thankyou kindly! ...
written 22 months ago by kjb32210
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MPileup calling every base as <X>
... Having a few teething problems on my first use of Galaxy (surprise!)   Workflow as follows; Upload fastq files (forward and reverse) Fastq groomer Trimmomatic BWA SAM to BAM MPileup ANNOVAR   ANNOVAR gives an empty vcf file and on closer inspection, MPileup gives 55,000,000 lines form 3,6 ...
mpileup galaxy alignment bwa help written 22 months ago by kjb32210

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