User: Yang Liao

gravatar for Yang Liao
Yang Liao70
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70
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Location:
Australia
Last seen:
2 months ago
Joined:
5 years, 1 month ago
Email:
l***@wehi.edu.au

Posts by Yang Liao

<prev • 8 results • page 1 of 1 • next >
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Comment: C: makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGen
... I'm facing the same problem and I found that the makeTxDbFromGFF() function already dropped the exons if they span multiple chromosomes and/or multiple strands. I built a GTF file that contains only four exons from one gene, but from different strands of chr1. The makeTxDbFromGFF() function gave wa ...
written 8 weeks ago by Yang Liao70
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... Thanks for the detailed explanation! Yes, I can now reproduce the error by adding "-O 0" to the compiler parameters. It is a little surprising to see that an optimisation option can change the legitimate behaviour of the compiler. I have removed this keyword from my codes.  ...
written 3 months ago by Yang Liao70
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Answer: A: Rsubread install fails, "unable to load shared object Rsubread.so"
... I understand that the "inline" keyword instructs the compiler to embed the function into all its callers, and modern compilers are smarter to automatically make the decision, leaving this keyword obsolete. However, it should be harmless when you build a shared object from the codes including inline ...
written 3 months ago by Yang Liao70
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Comment: C: Rsubread featureCounts with byReadGroup
... Thanks! I've downloaded the data, and found that featureCounts had a bug in the routine for fixing the BAM format. It did not keep the read group names when fixing the BAM files from Picard or STAR.  This bug has been fixed. The next released version should work on your BAM files. Cheers, Yang ...
written 11 months ago by Yang Liao70
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Comment: C: Rsubread featureCounts with byReadGroup
... It still works when I converted the SAM file to BAM by using Picard (SortSam). Is it possible if you can send us the BAM file you're using?  Cheers, Yang # /picard-tools-2.9.4/bin/SortSam I=user-RG.bam o=user-RG-Picard.bam SO=coordinate > x<-featureCounts(c('user-RG.bam','user-RG-Picar ...
written 11 months ago by Yang Liao70
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Answer: A: Rsubread featureCounts with byReadGroup
... Hi Ge Tan, I used Rsubread_1.26.1 to assign the lines you provided, and the read groups were correctly treated by featureCounts: x<-featureCounts(c('user-RG.bam','user-RG.sam') , annot.inbuilt = "hg19", byReadGroup = T) NCBI RefSeq annotation for hg19 (build 37.2) is used. //================= ...
written 11 months ago by Yang Liao70
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Answer: A: Error with featureCounts
... It looks that the current directory has no enough space, or some reads in the SAM file are extremely long (e.g., longer than 1200 bps).  ...
written 3.6 years ago by Yang Liao70
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Answer: A: Rsubread - featureCounts for extracting read counts from De novo assembled trans
... Dear Alan, Thank you for using Rsubread. The number of transcripts in the annotation file would not be an issue -- our featureCounts function supports unlimited number of annotations and chromosomes/transcripts (actually, at most 2 billions). I have just tried to run the in-development version of ...
written 5.1 years ago by Yang Liao70

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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Rsubread install fails, "unable to load shared object Rsubread.so"

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