User: Wei Shi

gravatar for Wei Shi
Wei Shi2.8k
Reputation:
2,780
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
1 day, 7 hours ago
Joined:
10 years, 11 months ago
Email:
s**@wehi.edu.au

Laboratory Head, Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Posts by Wei Shi

<prev • 330 results • page 1 of 33 • next >
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Answer: A: Low number of assigned reads using featureCounts / Strandedness issue
... Your counting result is perfectly as expected. What is your question here? You used dUTP protocol which sequenced the reverse strand of genes and strandSpecific=2 gives you exactly what you expect to get. So your sequencing works well and your counting works well too. ...
written 1 day ago by Wei Shi2.8k
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Comment: C: Rsubread Installation error
... I don't know what caused this problem. You tried to install Rsubread version 1.28.1 on R 3.3.3, but this version of Rsubread is released with R 3.4.3. Not sure if it is the difference in R version causing this compilation problem. ...
written 8 days ago by Wei Shi2.8k
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Comment: C: featureCounts taking 4-10 hours per BAM file?
... Please update your Rsubread and R to the latest version. Your Rsubread is two versions older than its latest release. A lot of improvements have been made to improve the speed of counting location-sorted pair-end reads in recent versions. ...
written 8 days ago by Wei Shi2.8k
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Comment: C: Create count matrix with featureCounts for stranded as well as reversely strande
... Yes you would need to count the two types of reads separately and then combine them (it should be straightforward to combine them). But we will add support to allow strandSpecific to have a vector value. ...
written 9 days ago by Wei Shi2.8k
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Comment: C: nthreads option does NOT work in rsubread featureCounts
... Thanks for the suggestion. We will have an investigation about this. ...
written 12 days ago by Wei Shi2.8k
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Answer: A: Create count matrix with featureCounts for stranded as well as reversely strande
... You don't have to count your PE and SE bam files separately. featureCounts automatically detects if your bam files contain SE or PE reads. You can provide all your bam files to featureCounts in one go and set isPairedEnd=TRUE. featureCounts will count number of reads pairs for your PE bam files and ...
written 12 days ago by Wei Shi2.8k
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Answer: A: Rsubread Installation error
... The compilation errors are caused by the use of compiler 'icc'. Rsubread has been comprehensively tested on compiler 'gcc' but not on 'icc'. I think you will probably have to switch to gcc for compiling Rsubread. The following page provides useful advice for how to do so: https://stackoverflow.com ...
written 14 days ago by Wei Shi2.8k
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Answer: A: problem of getting count matrix in featurecounts of Rsubread package
... As Gordon pointed out, your GTF file does not contain gene identifier attribute gene_id. The gene identifier attributes provided in your GTF file include ID and Parent. I think you should set GTF.attrType="ID" to get gene-wise counts. ...
written 8 weeks ago by Wei Shi2.8k • updated 8 weeks ago by Gordon Smyth33k
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Comment: C: Rsubread Read Bam and filter reads by TAG field
... Sorry for my slow response. However I am not quite sure what feature you request here. As far as I know reads from each single cell are often organized as a read group in a bam file. Is the 'byReadGroup' option in featureCounts what you are after? ...
written 11 weeks ago by Wei Shi2.8k
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Comment: C: caught segfault when using featureCounts
... This is now fixed in both release and devel versions. ...
written 3 months ago by Wei Shi2.8k

Latest awards to Wei Shi

Popular Question 11 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 11 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.0 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.0 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.0 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.2 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Use BAM file created from subjunc function (Rsubread package) for feature counts
Scholar 2.3 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Use BAM file created from subjunc function (Rsubread package) for feature counts
Scholar 2.8 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.9 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 3.4 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 3.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 3.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 3.6 years ago, created 100 posts.

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