User: dec986

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dec986130
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Posts by dec986

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Comment: C: samtools sort doesn't finish sorting bam file, just hangs for hours
... 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 dec986130
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samtools sort doesn't finish sorting bam file, just hangs for hours
... 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 ...
samtools written 7 weeks ago by dec986130
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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 5 months 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 5 months 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 5 months 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 5 months ago by dec986130 • updated 5 months 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 5 months 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 5 months 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 5 months ago by dec986130 • updated 4 months 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 5 months ago by dec986130

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Popular Question 5 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 5 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
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Teacher 9 months ago, created an answer with at least 3 up-votes. For A: [Opinion] - What alignment software do you use?
Popular Question 10 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
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Scholar 14 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool
Popular Question 21 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 21 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 21 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool

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