User: lim.michelle.25

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Posts by lim.michelle.25

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(Closed) Intersect more than two vcf files
... Hi everyone, I have nine vcf files that I'd like to intersect. I want to know which, if any, genes are commonly mutated across all nine samples. Is there a way to do this either on galaxy or using command lines? Thank you! ...
intersect galaxy written 2 days ago by lim.michelle.250
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How to intersect vcf files for commonly mutated genes only (not the exact mutation)
... Hi all, I intersected two vcf files using vcf-vcf intersect on usegalaxy.org and I realized that I'm not getting as many results because the program looks for exact mutations between two vcf files (ex. Jak3 arginine to histidine at amino acid position 653). What I want is to be able to look for gen ...
galaxy intersect vcf mutation written 2 days ago by lim.michelle.250 • updated 1 day ago by Jennifer Hillman Jackson25k
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Answer: A: SamToFastq: SAM validation error
... Hi Jen, Thanks for your reply. The AddOrReplaceReadGroups didn't work. I will contact the authors. Best, Michelle ...
written 27 days ago by lim.michelle.250
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SamToFastq: SAM validation error
... Hi all, I am new here, and also very new to galaxy. I'm trying to convert bam files to fastq using Picard's SamToFastq on galaxy. I've never had a problem doing this with my own whole exome sequencing bam files. But today I am using bam files downloaded from this link: http://sns.ias.edu/~cschan/TL ...
samtools galaxy written 28 days ago by lim.michelle.250

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