User: Ge Tan

gravatar for Ge Tan
Ge Tan20
Reputation:
20
Status:
New User
Location:
Switzerland
Last seen:
1 week ago
Joined:
2 years, 8 months ago
Email:
g*****@live.com

Posts by Ge Tan

<prev • 11 results • page 1 of 2 • next >
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Comment: C: caught segfault when using featureCounts
... Many thanks for fixing this. ...
written 21 days ago by Ge Tan20
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Comment: C: caught segfault when using featureCounts
... I changed as you suggested. ...
written 8 weeks ago by Ge Tan20
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caught segfault when using featureCounts
... Hi, I encountered segfault when calling featurecounts with Ensembl GRCh37 gtf file. In my dataset, only one bam file has the segfault, not the others. And if I use featurecounts in built NCBI RefSeq annotation hg19, it works, although the chromosomes are in chr* format, instead of Ensembl format. Th ...
rsubread featurecounts written 8 weeks ago by Ge Tan20
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Comment: C: Rsubread featureCounts with byReadGroup
... Super! Many thanks. Ge ...
written 4 months 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 4 months 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 4 months 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 4 months ago by Ge Tan20 • updated 4 months 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 4 months 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 16 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 2.3 years ago by Ge Tan20

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