User: Ge Tan

gravatar for Ge Tan
Ge Tan20
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Status:
New User
Location:
Switzerland
Last seen:
5 days, 10 hours ago
Joined:
2 years, 5 months ago
Email:
g*****@live.com

Posts by Ge Tan

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Rsubread featureCounts with byReadGroup
... Super! Many thanks. Ge ...
written 4 weeks ago by Ge Tan20
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Comment: C: Rsubread featureCounts with byReadGroup
... You can download the bam from https://1drv.ms/u/s!Ar4vJvgFbg4Ki8IqTmvwZ1kh8pGgXA Many thanks! Ge ...
written 6 weeks ago by Ge Tan20
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Comment: C: Rsubread featureCounts with byReadGroup
... Many thanks Yang! I used external Ensembl annotation. Here's the minimal command. featureCounts("merge_alignments_sorted.bam", annot.inbuilt=NULL, annot.ext="/srv/GT/reference/Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_89-2017-05-31/Genes/genes.gtf", isGTFAnnotationFile=TRUE, GTF.featureType ...
written 6 weeks ago by Ge Tan20
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Rsubread featureCounts with byReadGroup
... I have Rsubread 1.26.1 installed in order to do featureCounts with byReadGroup=TRUE. But featureCounts complains with "No read groups are found; no output is generated". || Process BAM file merge_alignments.bam... || || Single-end reads are included. ...
rsubread featurecounts written 7 weeks ago by Ge Tan20 • updated 6 weeks ago by Yang Liao20
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Answer: A: Error: unable to find an inherited method for function searchSeq for signature m
... You can manually create the PWMatrix class. PWMatrix(ID="Unknown", name="CTCF", matrixClass="Unknown", strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25), tags=list(), profileMatrix=pwm, pseudocounts=numeric()) ...
written 8 weeks ago by Ge Tan20
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Answer: A: Errore: subscript contains NAs - when running searchPairBSgenome in TFBTools
... Thanks for the report. This has been fixed in both release and development branches and will appear on Bioconductor soon. ...
written 13 months ago by Ge Tan20
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Answer: A: TFBSTools access to JASPAR2014 via getMatrixSet()
... Hi Jason, In JASPAR database, we occasionally update the matrices, hence several versions may exist for certain profiles. Generally, you can just set all_versions=FALSE. I will update the manual for better clarification.   Sorry for the confusion. Ge ...
written 2.1 years ago by Ge Tan20
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Answer: A: TFBSTools pvalues function hangs on certain inputs
... Hi, sorry for this late reply. It doesn't hang, but indeed is much slower on case sitesetList[[57]]. Eventually it returns 0.0003068776. By default, pvalues utilise the CRAN package TFMPvalue to calculate the pvalue. I need to look into details why it's slow on certain cases. If you wish, pvalues( ...
written 2.5 years ago by Ge Tan20

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