User: rquigl01

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rquigl0110
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1 year, 9 months ago
Joined:
1 year, 10 months ago
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r*******@rams.shepherd.edu

Posts by rquigl01

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Calling variants help
... mpileup and unified genotyper. Freebayes works but it doesnt open in IGV ...
written 22 months ago by rquigl0110
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Comment: C: Calling variants help
... mpileup and unified genotyper. Freebayes works but it doesnt open in IGV ...
written 22 months ago by rquigl0110
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Comment: C: Calling variants help
... freebayes doesnt open in IGV. All it says is malformed header ...
written 22 months ago by rquigl0110
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Calling variants help
... Hello Galaxy Biostar, For the past three weeks I've been trying to call SNPs and INDELs on my NGS samples for a summer research project. I'm a college student and all of this is new to me, but I've learned so much in these past three weeks. So far I have put my fastq files through bowtie2 on galaxy ...
calling mpileup galaxy snps indels written 22 months ago by rquigl0110 • updated 22 months ago by bryantl90
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Answer: A: Cannot set metadata on .bcf output from mpileup
... I had this problem as well but it fixed itself when I clicked on edit attributes and typed "bcf" in the Annotation / Notes section. Hope this helps someone. ...
written 22 months ago by rquigl0110
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Comment: C: mpileup calling every ALT <X>
... on bcftools view, there is an option to skip sites where the REF field is not A/C/G/T, but my problem is in the ALT column. What option on bcftools are you referring to? ...
written 22 months ago by rquigl0110
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Comment: C: Joining multiple fastq files that are spread across two lanes
... Thank you for your help! ...
written 22 months ago by rquigl0110
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mpileup calling every ALT <X>
... Im using the mpileup application on galaxy and every base is being called with the ALT . It has 110,000,000 lines as well which seems to be too much. I'm just trying to call SNPs and INDELS. Here is a screenshot. https://gyazo.com/f70ca31ebd7d47421b4e702ae3cb91f3 Does anybody know what I am doing ...
mpileup galaxy written 22 months ago by rquigl0110 • updated 22 months ago by Jennifer Hillman Jackson24k
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Joining multiple fastq files that are spread across two lanes
... Here is a screenshot of my data https://gyazo.com/90183f5cc58ef9aed362658e24ebf9c1 I know how to concatenate files. I'm just not sure which files I should link together. As you can see from the screenshot, there are 5 R1's from lane one and 5 R1's from lane two. Same scenario for all of the R2's. D ...
galaxy concatenate fastq two lanes written 22 months ago by rquigl0110 • updated 22 months ago by Jennifer Hillman Jackson24k
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IGV read color question
... What do the colors correspond to on IGV? Most of my reads are red with very few gray and blue colors. What do these colors mean and are they used when variant calling with mpileup? ...
mpileup igv color written 22 months ago by rquigl0110

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