User: dec986

gravatar for dec986
dec98630
Reputation:
30
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New User
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United States
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9 hours ago
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2 years, 10 months ago
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Posts by dec986

<prev • 62 results • page 1 of 7 • next >
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How to repair *all* problems identified by FastQC?
... hello, I am downloading public data, and am running FastQC on a number of FASTQ files I've downloaded. I get reports like this: PASS Basic Statistics SRR2637682_1.fastq.bz2 PASS Per base sequence quality SRR2637682_1.fastq.bz2 PASS Per tile sequence quality SRR2637682_1.fastq.bz2 ...
rna-seq fastqc written 1 day ago by dec98630 • updated 1 day ago by novice760
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Comment: C: how to fix Kmer count from FastQC?
... There are no adapters according to FastQC ...
written 2 days ago by dec98630
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how to fix Kmer count from FastQC?
... hello, I've been running various trimming and QC tools, but none of them can correct the Kmer count which is given by FastQC. I've searched a lot on this question and can find no answer. how can I correct the bad Kmer count given by FastQC? thanks ...
rna-seq fastqc written 2 days ago by dec98630 • updated 2 days ago by realnewbie10
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Comment: C: Fastq-Dump Crashes, how to prevent besides continually restarting?
... unfortunately, EBI-ENA has different issues. The "Bulk Download Files" button produces an error on Firefox "The address wasn’t understood Firefox doesn’t know how to open this address, because one of the following protocols (jnlp) isn’t associated with any program or is not allowed in this context ...
written 4 days ago by dec98630
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Fastq-Dump Crashes, how to prevent besides continually restarting?
... Hello, I'm downloading public data files from NCBI using (for example) fastq-dump --split-files -F --bzip2 SRR2637659 > SRR2637659.out 2> SRR2637659.err however, these commands crash every 6 runs or so, and download very very slowly. So far the only solution is to simply start again w ...
ncbi sra fastq-dump written 4 days ago by dec98630
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Comment: C: Solutions to FastQC diagnosis of Micro-Satellites
... hi h.mon, did you mean `--split_spot` or `--split-3`? ...
written 10 days ago by dec98630
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Comment: C: Solutions to FastQC diagnosis of Micro-Satellites
... @chen and @h.mon I have written a program, because the NCBI page https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2532810 doesn't suggest anything about paired-end reads. Also, if I remember how paired-end reads work, there should be some indication of this in the SEQID lines of the file shoul ...
written 10 days ago by dec98630
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Solutions to FastQC diagnosis of Micro-Satellites
... Hello, I'm looking through some FastQC reports on public data I've downloaded. The reports are mediocre quality, and the trimmers aren't making a difference. I've discussed this with a colleague, who says that my problem is that many reads are showing overrepresentation in the middle of the seque ...
rna-seq fastqc written 11 days ago by dec98630
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BiSeq manual giving incompatible objects
... Hello, I'm attempting to use the BiSeq package, and following the examples in their manual. However, I am running into trouble with the `compareTwoSamples` function, which is supposed to take a `BSrel` object, but following the manual, this ends up being an `S4` object. Does anyone have any scrip ...
R biseq written 4 weeks ago by dec98630
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Comment: C: 'BiocParallel' did not register default BiocParallelParams
... this whole comment thread reminds me of a diatribe by Linus Torvalds (the Linus of Linux), just replace "C++" with "R", his words, not mine: "C++ is a horrible language. It's made more horrible by the fact that a lot of substandard programmers use it, to the point where it's much much easier to g ...
written 4 weeks ago by dec98630

Latest awards to dec986

Scholar 5 weeks ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool
Popular Question 8 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 8 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 8 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 8 months ago, created a question with more than 1,000 views. For edgeR: no residual df: Cannot estimate dispersion
Supporter 8 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq2 comparison failure
Scholar 19 months 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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