## User: S.k

S.k10
Reputation:
10
Status:
New User
Location:
Last seen:
2 years, 2 months ago
Joined:
2 years, 3 months ago
Email:
s*******@gmail.com

#### Posts by S.k

<prev • 9 results • page 1 of 1 • next >
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... Thank you for your help. I need to run the developer version of R/Bioconductor to get the changes? Any idea when this will be pushed out to official releases? ...
written 2.2 years ago by S.k10
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... Hi Federico, Thanks for your help. I am having another issue, which I have posted here: https://support.bioconductor.org/p/82341/   ...
written 2.2 years ago by S.k10
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... I am getting an error when trying to run the annotateClusters function from the wavClusteR pipeline. All the other steps in the pipeline work. It appears to be an issue with the plotting. Any ideas? This step is quite far down the analysis pipeline, so I am not sure what other items might be relevan ...
written 2.2 years ago by S.k10 • updated 2.2 years ago by federico.comoglio100
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... Federico, thanks for your help. I repeated the alignment on that test sample with bowtie, and was able to progress past the pipeline step in the OP which was previously giving an error. This is the alignment command I used (using only one of the paired reads): zcat ${tmp_fastq1_gz} | bowtie "$tmp_ ...
written 2.2 years ago by S.k10
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... This was a paired-end alignment to mm10 with bowtie2, the command used was something like this: bowtie2 --threads "$THREADS" --local -x "$Genome_path" -q -1 "${FASTQ_R1}.trim" -2 "${FASTQ_R2}.trim" | samtools view -@ "$THREADS" -Sb1 - | samtools sort -m 10G -@ "$THREADS" - "\$SAMPLEID" ...
written 2.2 years ago by S.k10
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... Federico, I installed the developer version of R 3.3 for OS X and tried it again, and got the same error with the same data set, using version 2.5.2 of wavClusteR. > countTable <- getAllSub( Bam, minCov = 10 ) Loading required package: doMC Considering substitutions, n = 1999, processing ...
written 2.2 years ago by S.k10
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... Sorry I haven't figured out yet how to force a download for v2.5.2, I see it listed here: https://www.bioconductor.org/packages/3.3/bioc/html/wavClusteR.html But when I run the commands listed : source("https://bioconductor.org/biocLite.R") biocLite("wavClusteR") It gives me the 2.4.1 version i ...
written 2.2 years ago by S.k10
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... Thanks for looking into this. I tried to change the tag but I think that the forum here is intentionally using lowercase for the tags. ...
written 2.3 years ago by S.k10
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... I am working on PAR-CLIP analysis using the wavClusteR package. When I try to load a bam file, I get the following error:   > filename<-("test.bam") > Bam <- readSortedBam(filename = filename) > Bam > countTable <- getAllSub( Bam, minCov = 10 ) Loading required package: doMC ...
written 2.3 years ago by S.k10 • updated 2.2 years ago by federico.comoglio100

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