User: Yang Liao

gravatar for Yang Liao
Yang Liao20
Reputation:
20
Status:
New User
Location:
Australia
Last seen:
2 weeks, 1 day ago
Joined:
4 years, 3 months ago
Email:
l***@wehi.edu.au

Posts by Yang Liao

<prev • 5 results • page 1 of 1 • next >
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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 5 weeks ago by Yang Liao20
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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 6 weeks ago by Yang Liao20
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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 7 weeks ago by Yang Liao20
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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 2.8 years ago by Yang Liao20
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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 4.3 years ago by Yang Liao20

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