User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.3k
Reputation:
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Location:
Germany
Twitter:
dpryan79
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4 hours ago
Joined:
2 years ago
Email:
d*******@gmail.com

Bioinformatician / data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany. I'm one of the developers for deepTools (among other packages).

Posts by Devon Ryan

<prev • 228 results • page 1 of 23 • next >
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Comment: C: Normalization of RNA-seq data
... Generally one does this in comparison to other samples (e.g., with edgeR or DESeq2 in R). This is generally the most robust method. ...
written 7 hours ago by Devon Ryan1.3k
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Comment: C: htseq-count did not work
... "Did not work" as in results in an error or something else? If nothing else, use featureCounts instead (it's much faster). ...
written 1 day ago by Devon Ryan1.3k
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Comment: C: Running DESeq2 inside local Galaxy instance
... What version of Galaxy are you using? If you're using anything recent, switch to conda for dependency resolution and call it done. For me that's saved a LOT of headaches. ...
written 2 days ago by Devon Ryan1.3k
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Answer: A: remove in mapping results the reads that aligned > 1 times
... You can use the "Filter SAM or BAM, output SAM or BAM" tool under "NGS: Samtools". Just set the "Minimum MAPQ quality score" (the "quality" is redundant in that label...) to 2. This will remove slightly more than just those alignments that align >1 times, but the difference is minor (if you wante ...
written 3 days ago by Devon Ryan1.3k
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Comment: C: HELP!! BAM file shows one line analysis with zero values when "bam coverage" is
... I replied to this via email, but the cause of the problem was that the BAM file (for whatever reason) only had alignments on chr1. ...
written 7 days ago by Devon Ryan1.3k
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Comment: C: HELP!! BAM file shows one line analysis with zero values when "bam coverage" is
... Have you looked at the BAM file in IGV? Perhaps what you're seeing is the appropriate result. ...
written 11 days ago by Devon Ryan1.3k
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Comment: C: what is thye meaning of too low aQual in Htseq
... There's no reason to restrict htseq-count to CDS. Intergenic counts are the `no_feature` number. There will always be a fair number of those, mostly from background transcriptional noise. ...
written 26 days ago by Devon Ryan1.3k
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Answer: A: what is thye meaning of too low aQual in Htseq
... `aQual` is supposed to mean the alignments mapping quality score (aka, the MAPQ). You can instruct bowtie to include unaligned reads in its output, in which case you'll see them mentioned in the htseq-count output. Additionally, many reads will map to intergenic regions, which may also be what you' ...
written 27 days ago by Devon Ryan1.3k
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Comment: C: negative and positive fold change for a set of unigenes with similar gene ids i
... I presume you're seeing two transcripts of what is really a single gene (that or it became two separate genes in the organism you're looking at). ...
written 27 days ago by Devon Ryan1.3k
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Answer: A: HTSeq-count, maximum buffer size exceeded
... There's nothing you can do to prevent this from happening. If the instance of Galaxy you're using has featureCounts installed, then use it instead. ...
written 5 weeks ago by Devon Ryan1.3k

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