User: boyu93

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boyu9310
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Posts by boyu93

<prev • 11 results • page 1 of 2 • next >
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Comment: C: What is the reasonable proportion of zero counts in single-cell RNA-Seq data
... These methods should be useful when evaluating the cluster/ imputation methods. However, I hope to know if there is an approximate zero count rates. Normally, in sc-RNA seq, zeros occupy 80% due to drop-out issue. But the zero expression rate of the true data is not known. ...
written 6 days ago by boyu9310
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What is the reasonable proportion of zero counts in single-cell RNA-Seq data
... Due to the drop-out issue, in the expression matrix, there are a lot of zero counts in the sc-RNA Seq. But if without drop-out, what value of the proportion of zero counts should be reasonable? I couldn't find any knowledge on this. Does anyone have any idea on this? ...
single-cell rna-seq single-cell rna-seq sc-rna written 9 days ago by boyu9310 • updated 9 days ago by spacemorrissey180
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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 4 months ago by boyu9310
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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 4 months ago by boyu9310
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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 4 months ago by boyu9310 • updated 4 months ago by Denise - Open Targets4.5k
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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 5 months ago by boyu9310
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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 6 months ago by boyu9310
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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 6 months ago by boyu9310
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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 6 months ago by boyu9310 • updated 6 months ago by Pierre Lindenbaum110k
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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 7 months ago by boyu9310

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