User: Carolin Walter

Reputation:
10
Status:
New User
Location:
Germany
Last seen:
2 years ago
Joined:
4 years, 1 month ago
Email:
c*************@uni-muenster.de

Posts by Carolin Walter

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Basic4Cseq wiggle function
... Hi, ok, did you mask the actual chromosome identifier in your output data, or does your original data indeed say "chr" (and not "chr1", or "chr12"...)? If it's the latter, this may be the reason for the wig export problem. Could you please check if the chromosome identifiers look "normal" when you ...
written 4 months ago by Carolin Walter10
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Answer: A: Basic4Cseq wiggle function
... Hi, the read distribution looks good, so the data should be imported correctly. Could you please check what happens if you use exportVisualizationFragmentData with your data? The output should be a simple csv file with "chrom", "start", "end", and "reads". If that looks strange (as in "empty", or " ...
written 4 months ago by Carolin Walter10
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Comment: C: error while running Basic4CSeq
... Hi Tal, sorry for the delay (again), my e-mail notification seems to miss questions/comments when the package name is misspelled (in this case, Basic4CSeq instead of Basic4cseq). As said before, if everything seems to be fine (1...Y or chr1...chrY everywhere, etc), please feel free to contact me d ...
written 3.0 years ago by Carolin Walter10
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Answer: A: Basic4Cseq, degenerate sites
... Hi, I'm sorry, but Basic4Cseq doesn't support degenerate sites. I tried a simple approach for this problem months ago, and it caused more trouble than it was worth. Since I can't promise to solve this issue in the near future, I'd suggest using another algorithm for your data. Best, Carolin ...
written 3.0 years ago by Carolin Walter10
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Answer: A: error while running Basic4CSeq
... Hi Shruti, sorry for the delay in response, and sorry for the problem that you encountered. The "tempPlus < 0" error is usually caused by a mismatch of chromosome annotations, e.g. "1,2,...X,Y" in your reference genome and "chr1, chr2...chrX, chrY" in your virtual fragment library. The function ...
written 3.5 years ago by Carolin Walter10

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