User: JK

gravatar for JK
JK10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
4 years, 2 months ago
Joined:
4 years, 11 months ago
Email:
j************@genzyme.com

Posts by JK

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Issues parsing workspace in openCyto
... Issue is resolved. wsp format from FlowJo did not work. Had to use xml export of workspace.  ...
written 4.2 years ago by JK10
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Comment: C: Issues parsing workspace in openCyto
... I tried already; it did not solve the issue. I have been trying a couple of things. The issue may be related to the version of FACSDiva used on the machine for acquiring my data. The data I have been trying to parse is from a BD Influx. ...
written 4.2 years ago by JK10
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Issues parsing workspace in openCyto
... Hi, I am trying to parse a workspace in openCyto and getting the error message below:   > ws FlowJo Workspace Version  20.0 File location:  . File name:  20150714_b.wsp Workspace is open. Groups in Workspace          Name Num.Samples 1 All Samples           1 > gs=parseWorkspace(ws) Choos ...
opencyto written 4.2 years ago by JK10
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Comment: C: Error message from 'scanForHeterozygotes' function in AllelicImbalance package
... Yes, this issue is resolved. Thank you. ...
written 4.4 years ago by JK10
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Comment: C: Error using 'scanForHeterozygotes' function in AllelicImbalance package
... Thank you for resolving this issue. ...
written 4.4 years ago by JK10
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Error using 'scanForHeterozygotes' function in AllelicImbalance package
... Hi,   I generated BAM files using the STAR aligner. I am having some issues working with these BAM files in AllelicImbalance:   I would appreciate some help with the issue.   Best,   Jozsef > pathToFiles='h:/AGP_hg19_filtered_fastq_bam' > searchArea<-GRanges(seqnames = c("chr11"), ...
allelicimbalance written 4.6 years ago by JK10 • updated 4.4 years ago by Jesper Robert Gadin20
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Error message from 'scanForHeterozygotes' function in AllelicImbalance package
... I generated BAM files using the STAR RNA-Seq aligner and the work stream described in GATK:   https://www.broadinstitute.org/gatk/guide/article?id=3891   My R command with the error I am running into with these BAM files:   > heterozygotePositions <- scanForHeterozygotes(reads, maxReads= ...
allelicimbalance written 4.7 years ago by JK10 • updated 4.4 years ago by Jesper Robert Gadin20
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Comment: C: AllelicImbalance error with getAlleleCounts
... Valerie, I appreciate the email. I solved the issue. I was trying to read in a single bam file instead of a set of bam files. Regards, Jozsef On Jan 27, 2015, at 11:11 AM, Valerie Obenchain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a pos ...
written 4.7 years ago by JK10
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AllelicImbalance error with getAlleleCounts
... Hi,   I would appreciate some help with the error below. I am trying to process Bowtie2-aligened and subsequently Rsamtools sorted and indexed bam files with the package AllelicImbalance according to the manual on the Bioconductor page. I am getting the error below: > searchArea <- GRanges( ...
allelicimbalance getallelecounts written 4.7 years ago by JK10 • updated 4.7 years ago by Valerie Obenchain6.7k
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AlleicImbalance error reading in BAM files
... Hi,   I have bam files generated by using Bowtie2 and samtools. I am getting the following error message when trying to use the package AllelicImbalance: I would appreciate help on why this happens. Thank you, Joe > reads <- impBamGAL(pathToFiles,searchArea,verbose=FALSE) Error in FUN(" ...
allelicimbalance written 4.8 years ago by JK10 • updated 4.8 years ago by Martin Morgan ♦♦ 23k

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Popular Question 4.2 years ago, created a question with more than 1,000 views. For Estimation of dispersion in DeSeq and DeSeq2

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