User: dec986
dec986 • 130
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Posts by dec986
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... indeed, the issue was disk space, silly me. It would have been nice had samtools provided an error, however, the temp files used more space than I anticipated. ...
written 7 weeks ago by
dec986 • 130
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... I am trying to sort a bam file, which is 4.1 GB in size using simply `samtools sort -o sorted.bam start.bam`, but the file hangs after about 6.5 hours when the sorted file is 3.1 GB, no warning messages or anything. None of the temp files have been deleted either. I don't think the computer ran ou ...
written 7 weeks ago by
dec986 • 130
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... I've edited the original question to show how I'm running ballgown ...
written 5 months ago by
dec986 • 130
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... thanks, I've edited the original post ...
written 5 months ago by
dec986 • 130
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... 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 5 months ago by
dec986 • 130
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... 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", ...
written 5 months ago by
dec986 • 130
• updated
5 months ago by
sanchi.andrea • 0
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... 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 5 months ago by
dec986 • 130
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... 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 5 months ago by
dec986 • 130
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... 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 ...
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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 5 months ago by
dec986 • 130
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