User: Wei Shi

gravatar for Wei Shi
Wei Shi2.9k
Reputation:
2,910
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Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
13 hours ago
Joined:
11 years, 3 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 • 351 results • page 2 of 36 • next >
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... The inbuilt annotation was built based on NCBI RefSeq annotation so chr names should match between your mapped reads and the inbuilt annotation. What kind of sequencing data you are analyzing?   ...
written 3 months ago by Wei Shi2.9k
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Did you map your reads to mm10? Have you checked if the chr names in your reference genome match those in the annotation? ...
written 3 months ago by Wei Shi2.9k
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Could you show the counting summary by issuing the following command? This will tell you the reasons why most reads were not counted. fc_PE$stat ...
written 3 months ago by Wei Shi2.9k
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... Thanks Martin. ...
written 3 months ago by Wei Shi2.9k
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Answer: A: lncRNA annotation for featureCouns and STAR
... Aligners like STAR, TopHat and Subread use an annotation to assist the mapping of RNA-seq reads. Since your data is total RNA sequencing data, it makes more sense to me to use a transcriptome annotation in your read mapping instead of a lncRNA annotation. You can then count mapped reads to lncRNAs u ...
written 3 months ago by Wei Shi2.9k
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... The 'Rsubread.so' file was successfully generated and the compilation seems to be OK. I dont know what caused the problem. Maybe try reinstall your R and then install Rsubread so you can install it in a fresh session. ...
written 3 months ago by Wei Shi2.9k
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Comment: C: strange results with featureCounts
... If multi-overlapping alignments (alignment overlapping more than one gene) are included in the counting, then it is possible that column sums of count matrix are greater than the total number of alignments assigned by featureCounts because a multi-overlapping alignment gives rise to more than one co ...
written 3 months ago by Wei Shi2.9k
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... Can you provide the complete screen output from your installation? The 'Rsubread.so' file is generated after the gcc compilation is successfully completed. If the gcc compilation failed then you wouldn't get the Rsubread.so file generated and Rsubread won't be loaded. ...
written 3 months ago by Wei Shi2.9k
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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 4 months ago by Wei Shi2.9k
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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 4 months ago by Wei Shi2.9k

Latest awards to Wei Shi

Popular Question 3 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 3 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 14 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 14 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 14 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Popular Question 14 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 14 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 14 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 16 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 16 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 16 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 19 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.4 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.4 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.6 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.6 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 2.7 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.9 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 3.2 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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