User: Wei Shi

gravatar for Wei Shi
Wei Shi2.9k
Reputation:
2,890
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Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
11 hours ago
Joined:
11 years, 2 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 • 348 results • page 1 of 35 • next >
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Answer: C: File not found error when using dupRadar::analyzeDuprates
... This file path issue has been fixed in the recent Rsubread releases. Please update your Rsubread and R to their latest. The latest Rsubread version is 1.30.5. ...
written 15 days ago by Wei Shi2.9k
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Answer: A: Subread FeatureCounts for Exon level quantification: Length estimate for Exons a
... Have you looked into your GTF file to see if these exons are indeed very short? featureCounts just uses your provided annotation for counting and it does not modify your annotation. The counting percentage for your polyA sample from featureCounts sounds reasonable. I dont have much experience with ...
written 4 weeks ago by Wei Shi2.9k
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Answer: A: featureCounts for multiple features
... Regarding questions related to featureCounts that is released as part of the SourceForge Subread package, please send your question to Google Subread group (https://groups.google.com/forum/#!forum/subread). You cannot count reads to three different types of features at one time with your current GT ...
written 5 weeks ago by Wei Shi2.9k • updated 5 weeks ago by Gordon Smyth34k
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Comment: C: Rsubread Installation error
... If the issue you encountered is the same as the issue reported above, then have you checked if your Rsubread version matches the version of R?   ...
written 5 weeks ago by Wei Shi2.9k
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Comment: C: read count summed over exons is greater tham the gene-level read count using fea
... Yes this should make total exonic counts be less than total counts for genes. However this will result in the loss of exon-spanning reads and your exonic counting result wouldn't be as accurate.  What is the problem with getting more counts for exons? You have to count all the reads originating fro ...
written 7 weeks ago by Wei Shi2.9k
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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 8 weeks ago by Wei Shi2.9k • updated 8 weeks ago by Gordon Smyth34k
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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 9 weeks ago by Wei Shi2.9k
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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 9 weeks 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 9 weeks 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 9 weeks ago by Wei Shi2.9k

Latest awards to Wei Shi

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 11 weeks ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 13 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 13 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 13 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
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
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: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 13 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 15 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 15 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 15 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 18 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.3 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.3 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.5 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 2.6 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: Use BAM file created from subjunc function (Rsubread package) for feature counts
Scholar 3.1 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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