User: Wei Shi

gravatar for Wei Shi
Wei Shi2.8k
Reputation:
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Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
1 day, 21 hours ago
Joined:
11 years 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 • 343 results • page 2 of 35 • next >
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Comment: C: strange results with featureCounts
... The assignment percentage is typically around 50 - 70 percent. So your percentages are a bit low but not unusual. The percentage tends to be lower when multi-mapping reads are included. ...
written 5 weeks ago by Wei Shi2.8k
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Answer: A: strange results with featureCounts
... FeatureCounts reports number of alignments whereas STAR reports number of reads (number of reads pairs in this case since the data is paired end). The reporting of a mapped read may include one or more alignments. A uniquely mapped read will lead to the reporting of one single alignment, but a multi ...
written 5 weeks ago by Wei Shi2.8k
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Comment: C: Low number of assigned reads using featureCounts / Strandedness issue
... Yes the setting of strandSpecific parameter is only determined by the sequencing protocol used. It has nothing to do with the reads being single ended or pair ended. If you are unsure about the type of stranded data generated you should talk to the person who conducted the library prep to get this ...
written 8 weeks ago by Wei Shi2.8k
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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 8 weeks 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 9 weeks 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 9 weeks 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 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Wei Shi2.8k

Latest awards to Wei Shi

Popular Question 12 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 12 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Scholar 12 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 12 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 12 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Scholar 12 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Popular Question 13 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 13 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 13 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 16 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.2 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.2 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.4 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 2.4 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Scholar 2.4 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.7 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 3.0 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 3.1 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 3.6 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 3.6 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?

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