User: laurabuggiotti

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Posts by laurabuggiotti

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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... Hi again, i did try various bam files and it seems that the error occurs when using recalibrated bam files (after the BQSR step)...do you reckon there might be a link with the issue? Did you ever experience the same issue? Thanks a lot for your time, Laura ...
written 20 hours ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... Ok..this is what i did: > bamFile <- open(BamFile("bamKorea/A27.realigned.rmdup.bam")) > bamFile class: BamFile path: bamKorea/A27.realigned.rmdup.bam index: bamKorea/A27.realigned.rmdup.bai isOpen: TRUE yieldSize: NA obeyQname: FALSE asMates: FALSE > BAMFiles = ("bamKorea/SAMN0222573 ...
written 4 days ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... i have tried with one bam file as you suggested: Tracing open.BamFile(BamFile(file, character(0))) on entry [1] "/users/lbuggiotti/bamKorea/A27.realigned.rmdup.bam" Identified the following reference sequences: Chr1,Chr2...... ..... Missing "refSeqNames"! Selecting all identified reference seque ...
written 4 days ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... yes, it is in the same directory, here one example of the name: A27.realigned.rmdup.bai A27.realigned.rmdup.bam and got no error when opening the bam file as you suggested (via Rsamtools). anything else you could think of?   ...
written 4 days ago by laurabuggiotti0
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Answer: A: cn.MOPs: Error in value[[3L]](cond) :
... Thanks for your prompt answer, here is the traceback: > traceback() 11: stop("failed to open BamFile: ", conditionMessage(err)) 10: value[[3L]](cond) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch({ .io_check_exists( ...
written 4 days ago by laurabuggiotti0
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cn.MOPs: Error in value[[3L]](cond) :
... Hi, I have been using cn.mops successfully using the following commands: bamDataRanges <- getReadCountsFromBAM(BAMFiles, refSeqName=readLines("Chr_list.txt"), WL=1000) results <- calcIntegerCopyNumbers(cn.mops(bamDataRanges)) segm <- as.data.frame(segmentation(results)) CNVs <- as.d ...
cn.mops written 5 days ago by laurabuggiotti0 • updated 4 days ago by Günter Klambauer510
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cn.mops: interpreting output when returnPosterior=TRUE
... Hi, Im using cn.MOPS for detecting CNVs in multiple WGS samples, however i got some questions concerning the interpretation of the output: When using returnPosterior=TRUE should i have an additional column with a posteroir probability value or is the output filtered according to the latter? I ha ...
cn.mops written 10 weeks ago by laurabuggiotti0 • updated 10 weeks ago by Günter Klambauer510
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Errore: subscript contains NAs - when running searchPairBSgenome in TFBTools
... Hi, I am using TFBSTools with JASPAR2016 library to scan a pairwise alignment. The command im using is as follows: > sitePairSet <- searchPairBSgenome(pwm, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Oaries.UCSC.oviAri3, chr1="chr29", chr2="OAR21", min.score="80%", strand="*", chain=chain) Er ...
bioconductor tfbstools written 21 months ago by laurabuggiotti0 • updated 20 months ago by Ge Tan20
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Errore: subscript contains NAs - when running searchPairBSgenome in TFBTools
... Hi, I am using TFBSTools with JASPAR2016 library to scan a pairwise alignment. The command im using is as follows: > sitePairSet <- searchPairBSgenome(pwm, BSgenome.Btaurus.UCSC.bosTau6, BSgenome.Oaries.UCSC.oviAri3, chr1="chr29", chr2="OAR21", min.score="80%", strand="*", chain=chain) Err ...
software error written 21 months ago by laurabuggiotti0

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