User: Bio152

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Bio152150
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Posts by Bio152

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ExomeDepth Package Error Messages
... I am using the steps in the vignette to analyze my data. When I attempted Section 5, I received the following errors while using ExomeDepth's command:   > my.choice <- select.reference.set (test.counts = my.test, reference.counts = my.reference.set, bin.length = (ExomeCount.dafr$end - ExomeCo ...
cnv exome written 3.8 years ago by Bio152150
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Comment: C: DEXSeq update
... After properly sorting, using Simons method and then using the dexseq count program I get error messages These are a sample of the error messages: UserWarning: Read HWI-ST522:121:D0V1CACXX:8:1106:20332:74088 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted? ...
written 6.2 years ago by Bio152150
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DEXSeq update
... Hi Simon, It appears that one of my regular unsorted SAM files is truncated. Though the sort works fine and samtools view does not detect truncation in my file.sam.bam, I still get error messages after attempting to generate counts files. samtools view -h file.sam.bam | python dexseq_count.py fil ...
written 6.2 years ago by Bio152150 • updated 6.2 years ago by Simon Anders3.6k
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DEXSeq Paired-end analysis (new issues)
... Hi Simon, The sort code worked just fine. I also ran a diagnostic on the *.bam files and no error came up. But when I tried to use the sorted *.sam.bam file with the dexseq_count.py program, I got the following messages: [mlinan@s59-14 MISC]$ python dexseq_count.py -p yes -s no hs71.gff ahBC010. ...
written 6.2 years ago by Bio152150 • updated 6.2 years ago by Devon Ryan200
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DEXSeq: Paired End Analysis
... To All DEXSeq Users, I have BAM files which were created using Tophat. While I was able to create then sort my SAM files. I have been unsuccessful in getting the standard paired end code to work using python and htseq. Can anyone share the code they use to sort their SAM file and to successfully r ...
dexseq written 6.2 years ago by Bio152150 • updated 6.2 years ago by Simon Anders3.6k
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DEXSeq Help Needed: newExonCountSet() error messages
... Hi, I attempted to use the DEXSeq function newExonCountSet() and received this error message: > newExonCountSet(countData=counts(data), design=design(samples), geneIDs=geneIDs(data), exonIDs=exonIDs(data)) * Error in (function (classes, fdef, mtable) : unable to find an inherited method for ...
process dexseq written 6.4 years ago by Bio152150 • updated 6.4 years ago by Wolfgang Huber13k
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DEXSeq Question <|------Ignore, I figured it out.
... [[alternative HTML version deleted]] ...
written 6.5 years ago by Bio152150
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DEXSeq Question
... Dear Simon, Alejandro, etc I am trying to get the associated gene name printed next to the gene id column that is displayed on the HTML report created by the DEXSeqHTML function. I am aware there are options within the function, but I do not know how to use them to get the result that I am looking ...
written 6.5 years ago by Bio152150
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DEXSeq: Factor
... Hi Everyone, I encountered an error message from DEXSeq, and would like to know if someone else encountered it too and how they were able to fix the problem. Below is my code and error message: I have come across the following error. How do I prevent the error from occuring? Is it ok to use str ...
dexseq written 6.5 years ago by Bio152150
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DEXSeq troubles
... Hi- I have a new DEXSeq error that I could use help with: > samples=data.frame( + condition=c(rep("myfile", 1)), + row.names=file.path("/home/mlinan", pattern="myfile.counts"), + stringAsFactors=FALSE, + check.names= FALSE) > ecs = read.HTSeqCounts(countfiles = rownames(samples), design=samp ...
dexseq written 6.5 years ago by Bio152150 • updated 6.5 years ago by Alejandro Reyes1.7k

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