Gökalp Çelik
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Activity overview
Latest activity by Gökalp Çelik-
Gökalp Çelik commented,
Hi Konstantinos Voutetakis Depending on how and where you collect your sequencing samples from your cancer induced mice there may be different options for you. Firstly as mouse strains are usually...
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Gökalp Çelik commented,
Hi daytimemouse Looking at your charts I see that most of your mutations are around T>C or C>T. How was this data generated? Looks like bisulfite sequencing. Also you said you performed a germline ...
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Gökalp Çelik commented,
Hi If you are not discarding intronic variants that number is just about right since you are almost calling all genomic regions that are covered by reads. If you have an enriched library for mRNAs...
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Gökalp Çelik commented,
Hi Krishna I am glad that you have found the root cause. For those workflow/workload managers you can check their respective user support forums since we don't have resources to support them direct...
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Gökalp Çelik commented,
MarkIlluminaAdapters tool uses the built in list for --ADAPTERS if none specified. Under normal circumstances if the tool cannot detect any adapters from the specified list or the default list it w...
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Gökalp Çelik commented,
I am sure reads are present but how about the bed file? This error is thrown when there is no intersection between any interval parameters therefore it is possible that your bed file is missing tho...
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Gökalp Çelik commented,
Hi 周尤佳 You seem to be missing 2 additional parameters included in the best practices workflow. These parameters are included to filter out clustered events that may clutter your files. --cluster-s...
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Gökalp Çelik commented,
Hi Krishna Looking at your MarkIlluminaAdapters log tool seems to be facing with an empty bam file therefore it only takes 0.00 seconds to execute. Can you check your input files for integrity by u...
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Gökalp Çelik commented,
Hi Indrani Datta There will certainly be sessions about somatic analysis. Regards.
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Gökalp Çelik commented,
Here are the required parameters for GermlineCNVCaller step USAGE: GermlineCNVCaller [arguments]Calls copy-number variants in germline samples given their counts and the output of DetermineGermline...