User: jsalsager

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jsalsager40
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4 months, 1 week ago
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1 year, 8 months ago
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Posts by jsalsager

<prev • 14 results • page 1 of 2 • next >
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Answer: A: edger nearestTSS() fails saying NAs are not allowed in subscripted assignments
... Hey everyone, I got this solved. I wasn't removing all the nonstandard chromosomes. Adding the following line solved my issues: keep[ grep("hap",Chr) ] <- FALSE ...
written 6 months ago by jsalsager40
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Thanks so much Daniela! That did the trick!  You're the best!  :) ...
written 9 months ago by jsalsager40
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Thanks so much for your help! Here is a link I created for drop box. Paired end reads TEST_1.fastq.gz TEST_2.fastq.gz, each 100,000 reads. Simon    https://www.dropbox.com/sh/s5dw1cyfmikret8/AACWcOV2sX9WSsVMU3JIOMCxa?dl=0 ...
written 9 months ago by jsalsager40
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Thanks again for your help! So setting the batchsize=2 worked for the samples above. Interestingly enough, when I run my full fastq files with batchsize= anything but 1, it seems to fail. Each file has 50+ million reads. Think this is an issue with the paired end reads? One interesting note, I tri ...
written 9 months ago by jsalsager40
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Thanks for the feedback.  I tried my fastq.gz files separately and still ran into the issue. I took one set of reads and unzipped them, then removed the top 12 lines. When I ran them I saw the issue again. Is there anything obvious you see wrong with the following fastq files?  I really appreciate ...
written 9 months ago by jsalsager40
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Comment: C: Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... Hi @dcassol Thanks so much for getting back to me! I did try the demo data and it worked fine. Also, when I run the alignment with bowtie2 using the systemPipeR package using untrimmed fastq.gz files, it worked fine. The issue is only with preProcessReads(). I've tried everything I can think of so ...
written 9 months ago by jsalsager40
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Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
... > library(systemPipeR) Loading required package: Rsamtools Loading required package: GenomeInfoDb Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clus ...
systempiper written 9 months ago by jsalsager40
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Comment: C: How do I get groseq signal for each gene from groSeq in groHMM
... Can I bug you with one final question? If I wanted to export a similar file but using groHMM called transcripts rather than knownGenes, how would I change that code? I tried switching kgLimit with txLimit and ended up getting errors that I was combining a date.frame with different lengths. Thanks ...
written 11 months ago by jsalsager40
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Comment: C: How do I get groseq signal for each gene from groSeq in groHMM
... Thank you again, I really appreciate your help! ...
written 11 months ago by jsalsager40
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How do I get groseq signal for each gene from groSeq in groHMM
... hello! I worked my way through the tutorial for groHMM but I'm not sure how to get signal (RPKM, FPKM etc.) for each gene.  The tutorial just shows how to make graphs. Thanks! ...
grohmm groseq written 11 months ago by jsalsager40 • updated 11 months ago by anusha.nagari30

Latest awards to jsalsager

Scholar 9 months ago, created an answer that has been accepted. For A: edger nearestTSS() fails saying NAs are not allowed in subscripted assignments

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