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User: laurabuggiotti

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Posts by laurabuggiotti

<prev • 16 results • page 1 of 2 • next >
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cn.MOPS: Error in getReadCountsFromBAM
... Hi, Im trying to run cn.MOPS using multiple bam files of different breeds and while I can successfully run it by breed, when attempting to use all of them i get the following error: Error in getReadCountsFromBAM(BAMFiles, refSeqName = readLines("/users/lbuggiotti/WGresRussia/cn.MOPS/Chr_list.txt") ...
cn.mops written 5 months ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... when renaming the index file i dont get the error...thank you! Ill modify all indexes and i hope all the samples will be analysed with cn.MOPS. Thank you so much for your help! cheers, Laura ...
written 7 months ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... Tracing open.BamFile(BamFile(file, character(0))) on entry [1] "/users/lbuggiotti/bamKorea/SAMN02225733.realigned.rmdup.bam" [1] NA Tracing open.BamFile(BamFile(file, index), "rb") on entry [1] "/users/lbuggiotti/bamKorea/SAMN02225733.realigned.rmdup.bam" [1] "/users/lbuggiotti/bamKorea/SAMN02 ...
written 7 months ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... > BAMFile="bamKorea/SAMN02225733.realigned.rmdup.bam" >bamDataRanges <- getReadCountsFromBAM(BAMFile, refSeqName=readLines("/users/lbuggiotti/WGresRussia/cn.MOPS/Chr_list.txt"), WL=1000) I get the same error: Error in value[[3L]](cond) : failed to open BamFile: failed to load BAM in ...
written 7 months ago by laurabuggiotti0
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Comment: C: cn.MOPs: Error in value[[3L]](cond) :
... it doesnt complain: ​> open(BamFile("bamKorea/SAMN02225733.realigned.rmdup.bam")) > Im running the scan Bam at the moment and will need sometime... Rsamtools::scanBam("bamKorea/SAMN02225733.realigned.rmdup.bam")   ...
written 7 months ago by laurabuggiotti0
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Comment: C: cn.mops: bam BQSR file
... Hi Martin, thanks for answering...the error is the same as few days ago: Error in value[[3L]](cond) : failed to open BamFile: failed to load BAM index file: bamKorea/SAMN02225733.realigned.rmdup.bam In addition: Warning message: In doTryCatch(return(expr), name, parentenv, handler) : [bam_i ...
written 7 months ago by laurabuggiotti0
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(Closed) cn.mops: bam BQSR file
... Hi, I have been running cn.mops successfully and im in the need now to run it again using bam files retrieved from NCBI which are realigned BAM files after the recalibration step (BQSR) recommended from the best practices. I get an error pointing to the bam file, however the bam file is fine and o ...
cn.mops written 7 months ago by laurabuggiotti0
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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 7 months 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 7 months 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 7 months ago by laurabuggiotti0

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