User: dec986

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dec986130
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Posts by dec986

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Comment: C: how to get counts/TPM/etc. from stringtie?
... I've edited the original question to show how I'm running ballgown ...
written 10 weeks ago by dec986130
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Comment: C: how to get counts/TPM/etc. from stringtie?
... thanks, I've edited the original post ...
written 10 weeks ago by dec986130
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Comment: C: how to get counts/TPM/etc. from stringtie?
... hi @h.mon, I'm trying to make input for ballgown, and ballgown, and I have TPM info in the GTF files, but the problem is that ballgown doesn't see them. ...
written 10 weeks ago by dec986130
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how to get counts/TPM/etc. from stringtie?
... hello, I'm running stringtie to quantify transcripts on single-end RNA-Seq. how can I get stringtie to output more than FPKM and cov? Ballgown, which is meant for differential expression, gives options for inputting data in format ` "rcount", "ucount", "mrcount", "cov", "cov_sd", "mcov","mcov_sd", ...
rna-seq written 10 weeks ago by dec986130 • updated 10 weeks ago by sanchi.andrea0
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Comment: C: Differential Expression with Ballgown
... the issue that started this post was that stringtie has to be run with the "-e" option, without which the important transcripts will not appear. ...
written 10 weeks ago by dec986130
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Comment: C: Differential Expression with Ballgown
... yes, thanks, I looked at the stringtie output, and it appears that the problem is there. All key transcripts show 0 coverage. This is strange because featureCounts on the same bam files worked fine. I ran stringtie like `stringtie $bam -G $gtf -A $tab -o $out -B 2> $err` There is a wealth o ...
written 11 weeks ago by dec986130
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Differential Expression with Ballgown
... Hello, I've been attempting to run the Ballgown differential expression package, but am getting odd results. I have an experiment where a particular gene is knocked down, but it isn't showing as differentially expressed with Ballgown. I am comparing the results to EdgeR, and they are not coming ou ...
R rna-seq written 11 weeks ago by dec986130 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: R: Ballgown load fails
... thanks @cpad0112 that solved the problem. Simply, `sudo R` and then `install.packages('Rcurl')` ...
written 11 weeks ago by dec986130
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R: Ballgown load fails
... Hello, I updated my Ubuntu installation to 18.04 (support for 17.10 expired), and now I can no longer load Ballgown in R. I get the following error: con@con-VirtualBox:~/RNASeqb/Milanovich/genomeNext/compare$ Rscript pathfinder.ballgown.R Loading required package: methods Error: packa ...
software error R rna-seq written 11 weeks ago by dec986130
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Comment: C: STAR Alignment Score reduced after trimming
... Is there any official documentation for this? I can't find anything in google searches or in the STAR manual ...
written 12 weeks ago by dec986130

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
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