User: Vining, Kelly

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Vining, Kelly220
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Posts by Vining, Kelly

<prev • 22 results • page 1 of 3 • next >
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It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
... Hi Lukas, The first option appears to have worked! I have read in the first MEDIPS set. Following the tutuorial, it looks like additional biological reps get concatenated to the first one to make a list of MEDIPS sets. I'd like to read in all of my biological reps separately at first, though, becaus ...
alignment go cancer bsgenome rsamtools genomes medips written 3.6 years ago by Vining, Kelly220 • updated 3.6 years ago by Lukas Chavez470
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So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
... Thanks Lukas, Martin and Steve for all of your help. MEDIPS.createSet almost works now. Alas, I'm still getting an error. Troubleshooting these error messages is giving me a deeper understanding of what is going on at each step, and that is good, but I am ready to get this working once and for all. ...
alignment go cancer bsgenome rsamtools genomes medips written 3.6 years ago by Vining, Kelly220 • updated 3.6 years ago by Lukas Chavez470
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Comment: C: Rsamtools filtering bam file: RE: MEDIPS.createSet error
... It'll be great if I can simply use the chr.select parameter instead of creating a separate subset. I tried that, and it looks like it almost worked, but now I'm getting a different error: > budFall1_MEDIP = MEDIPS.createSet(file="FallBud_brep1_aln_sorted.bam", chr.select=seqnames(BSgenome), BSg ...
written 3.6 years ago by Vining, Kelly220
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Rsamtools filtering bam file: RE: MEDIPS.createSet error
... This is a follow-up question about the most efficient way to use functions in Rsamtools to filter my bam files so that only alignments to chromosomes are included (extrachromosomal scaffold alignments are excluded). >From the Rsamtools documentation, it looks like there are two ways to accomplis ...
go bsgenome rsamtools genomes medips written 3.6 years ago by Vining, Kelly220 • updated 3.6 years ago by Martin Morgan ♦♦ 20k
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Comment: C: MEDIPS.createSet error
... I see, Lukas. That makes sense. Thanks for explaining it. So, MEDIPS looks in the BSgenome object for seqnames only, and doesn't look in mseqnames. It seems like a lot of users of the MEDIPS package must encounter this problem, because most genomes have sets of unassembled scaffolds that, following ...
written 3.6 years ago by Vining, Kelly220
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MEDIPS.createSet error
... Thanks, Steve, for your advice - appreciate you working with a package that isn't familiar to you. Thanks also for catching that I didn't have Rsamtools installed. I think this output that you suggested I generate gives an idea about what might be going on: > si.bsg Seqinfo of length 19 seqnam ...
bsgenome rsamtools medips written 3.6 years ago by Vining, Kelly220 • updated 3.6 years ago by Lukas Chavez470
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Comment: C: MEDIPS.createSet error
... Hi, Thanks for the advice thus far! To confirm what is in my BSgenome variable, I did this: > class(BSgenome) [1] "BSgenome" attr(,"package") [1] "BSgenome" > names(BSgenome) [1] "Chr01" "Chr02" "Chr03" "Chr04" "Chr05" "Chr06" "Chr07" "Chr08" "Chr09" [10] "Chr10" "Chr11" "Chr12" "Chr13" "Chr ...
written 3.6 years ago by Vining, Kelly220
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Comment: C: MEDIPS.createSet error
... Hi Lukas, Well, I'm basically back to the original error I had when I started this work back in December. At that point, I'd decided that my bam files must have had chromosome or scaffold names that didn't exist in the reference genome. So I went back to the original data set and redid all of the al ...
written 3.6 years ago by Vining, Kelly220
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MEDIPS.createSet error
... Hello, I'm coming back to a MEDIPS project after a long pause, and am having trouble reading in my .bam files. I'm using a custom reference genome that Lukas Chavez kindly helped me to make into a BSgenome object. I'm not sure how to address the error message below. I hope it doesn't mean there is s ...
alignment bsgenome medips written 3.7 years ago by Vining, Kelly220 • updated 3.7 years ago by Lukas Chavez470
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Comment: C: Aha: different error may be a clue: RE: separate MEDIPS.createSet required for e
... That must be it!! The .bam files are archival data, so I'm 99% sure that chromosomes 1-9 have headers with single digits, like chr1..chr9, while my BSgenome object has chr01..chr09. OK, I have to go back to the alignment drawing board! That's fine...glad to have this resolved for the time being. Th ...
written 3.9 years ago by Vining, Kelly220

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