User: felix.klein

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felix.klein150
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Posts by felix.klein

<prev • 51 results • page 1 of 6 • next >
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Answer: A: FourCSeq Pipeline for Capture-C Data
... Hi Mark, entering the sequence twice might work. But you could also use another 4 cutter sequence. Reads will be counted at the ends of the first cutter used. The second cutter is used to define whether a fragment end is "valid" based on fragment size and whether there is a cutting site of the seco ...
written 7 weeks ago by felix.klein150
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Answer: A: FourCSeq - errors in plotZScores
... Hi Rustavo, right now I cannot tell what the problem is and from which function it is caused. Could you please run traceback() to track this down. Best regards, Felix   ...
written 13 months ago by felix.klein150
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Answer: A: FourCseq, rawRanges Description
... Hello Theodoros, these are a mixture from FourCSeq and DESeq2. For FourCSeq I can tell what they are, for DESeq2 you have to look it up in the documentation. leftSize/rightSize: Size of the left fragment end (1st to 2nd cutter site) leftValid/rightValid: Are the fragment ends valid (fragment of f ...
written 2.0 years ago by felix.klein150
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hello Theodoros, have a look at the dispersion fit whether this makes sense to you (plotDispEsts(fcf)). And have a look at the DESeq2 package which is behind all these calculations. Best regards, Felix ...
written 2.0 years ago by felix.klein150
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hello Theodoros, there should be not much more false "significat" contacts if you change the threshold within a reasonable range. What I meant with the switch in interaction differences is the following: If you use the plotDifferences function and see a clear trend that the log fold change is a ...
written 2.0 years ago by felix.klein150
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Comment: C: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hello Theodore, this seems like a quite high number. How many fragments are actually left after you used this threshold? You should definetly double check the results in this case because you probably remove quite a lot of fragments. Especially watch out if you have a switch in the interaction dif ...
written 2.0 years ago by felix.klein150
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Answer: A: FourCseq: mixed amount of replication/samples
... Hello Theodore, you can create the colDate in the way your experiment has been caried out. And if you have the required information in a csv file then you should use it as import. For simplicity I made use of the each function, but I could have used c(1,2, 1,2,3, ...) instead. Cheers, Felix ...
written 2.1 years ago by felix.klein150
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Answer: A: FourCseq: getZScores errors, first case 6 digenerated cutterm second case 4 base
... Hi Theodore, how do the scatter plots between your replicates look like? Do the libraries show sufficient agreement or are they quite different? As a straightforward approach you can try to increase the number in minCount. This will set aside low count fragments, which tend to have a higher noise ...
written 2.1 years ago by felix.klein150 • updated 2.1 years ago by Wolfgang Huber13k
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Answer: A: FourCseq- adding information manually
... Hi Tal, check that you have the same factor levels. I would assume, that fragemented_Rn6 has all chromosomes as level while colData only has chr5. If you add the missing levels there it should work. Best regards, Felix ...
written 2.1 years ago by felix.klein150
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Comment: C: local fit and FourCseq
... Hi Tal, this might indeed be to few fragments for the analysis. Did you have a look at the raw counts and how they are distributed? Also check the correlation plots with the different thresholds (after getZScores). How do they look? Best regards, Felix On 07/10/2016 03:03 PM, tlgolan [bioc] wr ...
written 2.1 years ago by felix.klein150

Latest awards to felix.klein

Scholar 2.8 years ago, created an answer that has been accepted. For A: FourCSeq - how to write tables with the results
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: FourCSeq - how to write tables with the results

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