User: boyu93

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boyu930
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Posts by boyu93

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Comment: C: Number of Transcripts in GRCh38
... Thanks so much for the reply. I just found that there were some problems using Tablemaker to process. The number of transcripts in the Tablemaker output is not consistent with the reference annotation. ...
written 7 weeks ago by boyu930
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Comment: C: Number of Transcripts in GRCh38
... Thank you so much! I found the information I needed. And I traced back to the annotation file used while running cufflinks. It seems that there's some mistake during either cufflinks or Tablemaker processing, which caused duplicated transcript names in a file. (Using Stringtie to process will not ...
written 7 weeks ago by boyu930
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Number of Transcripts in GRCh38
... I downloaded several canonical GRCh38 gtf files, but I found the number of transcripts are different in each gtf. I was hoping to find one with 198838 transcripts. Does anyone know where I could find a list showing the number of transcripts as to each version of canonical gtf file? **Edit**: I hav ...
genome rna-seq sequencing written 7 weeks ago by boyu930 • updated 7 weeks ago by Denise - Open Targets4.4k
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What is the meaning of Bumphunter output?
... I tried using ChAMP to analyze differential Methylation Regions (DMR).[ChAMP][1] The method I used was based on Bumphunter. But its output made me confused. Especially the difference between P.value and P.value.area. From the manual, I vaguely know that the former is based on simply comparing two sa ...
software methylation written 10 weeks ago by boyu930
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Popular Structural Variant Simulator
... I found there are a lot of SV simulators, which one is popular these days? Thanks! I know about two years ago, several outstanding papers used SVsim. ...
wgs structural variant dna written 3 months ago by boyu930
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Comment: C: Picard ValidateSamFile error
... Thank you so much! We found out that it was caused during copying into the disk, the file is not complete with only first several chromosomes included. I'd better check the completeness first in the future. ...
written 3 months ago by boyu930
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Picard ValidateSamFile error
... I wanted to run Breakdancer but received an error `EOF marker is absent`. So I tried Picard `ValidateSamFile` to see if there are any errors inside. When I run Picard `ValidateSamFile`, I received the following error: ValidateSamFile Value for tag MC is not a String: class java.lang.Integer I ...
picard bam written 3 months ago by boyu930 • updated 3 months ago by Pierre Lindenbaum106k
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Comment: C: Any techniques faster than Breakdancer?
... That's what I want to find in this link, a compile of SV caller packages. Thanks a lot natasha. ...
written 4 months ago by boyu930
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Any techniques faster than Breakdancer?
... I have been using Breakdancer for structural variant detection, but it is running so slow, which takes more than 30 hours for a pair of tumor/normal samples as to WGS data. Are there any other methods which can do similar stuff but run faster? Thanks, ...
sv breakdancer structural variant dna written 4 months ago by boyu930 • updated 4 months ago by Eric T.2.1k

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