User: Wei Shi

gravatar for Wei Shi
Wei Shi2.8k
Reputation:
2,820
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
12 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 1 of 35 • next >
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Answer: A: Is circular RNA read out as linear fragments during Rsubread-DESeq2
... If you used Rsubread featureCounts to generate counts, the mapped reads are just assigned to overlapping genes. It doesn't matter whether the genes are located on a linear sequence or on a circular sequence. ...
written 2 days ago by Wei Shi2.8k • updated 11 hours ago by Gordon Smyth33k
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Your analysis seems to be fine. You probably need to dig deeply into your reads to see where your reads are mapped to. Artifact/contamination in your sequencing or sample prep might cause an issue like this.   ...
written 6 days ago by Wei Shi2.8k
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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 7 days ago by Wei Shi2.8k
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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 8 days ago by Wei Shi2.8k
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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 9 days ago by Wei Shi2.8k
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... Thanks Martin. ...
written 21 days ago by Wei Shi2.8k
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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 22 days ago by Wei Shi2.8k
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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 24 days ago by Wei Shi2.8k
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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 27 days ago by Wei Shi2.8k
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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 27 days 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: Explainnation of featureCounts in-built annotation?
Scholar 11 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 11 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 11 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
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
Scholar 11 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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