User: Wei Shi

gravatar for Wei Shi
Wei Shi2.9k
Reputation:
2,910
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
13 hours ago
Joined:
11 years, 4 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 • 352 results • page 1 of 36 • next >
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Comment: C: Options Request for FeatureCounts
... Could you try the latest version? ...
written 20 days ago by Wei Shi2.9k
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Comment: C: Options Request for FeatureCounts
... As I explained in my reply above, a read is extended first and then it will be reduced to a single base. Regarding strandness filtering, you do not need to filter reads. You can directly filter counts by performing filtering on the object returned by featureCounts (strand info is included for every ...
written 7 weeks ago by Wei Shi2.9k
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Answer: A: Options Request for FeatureCounts
... You can use read2pos=5 together with readExtension5 to shift the 5' most base of a read to any position you want. The read is first extended upstream by number of bases specified by readExtension5, and then it is reduced to its new 5' most base. Note that the 5' most base can be shifted downstream a ...
written 7 weeks ago by Wei Shi2.9k
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Answer: A: Perfectly aligning sequences not mapping to worm genome in Subread's featureCoun
... First let me point out that featureCounts is not a read aligner. It is a read counting tool. Programs included in Subread package for read alignment are subread-align and subjunc. You may try the following to see if they can improve the mapping of your stress condition samples: (1) You do not need ...
written 8 weeks ago by Wei Shi2.9k
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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 11 weeks 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 3 months 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 3 months ago by Wei Shi2.9k • updated 3 months ago by Gordon Smyth35k
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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 3 months 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 3 months 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 4 months ago by Wei Shi2.9k • updated 3 months ago by Gordon Smyth35k

Latest awards to Wei Shi

Popular Question 4 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 4 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 15 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 15 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 15 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
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
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: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 15 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 17 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 17 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 17 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 20 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.5 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.5 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.7 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.7 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 2.8 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: Use BAM file created from subjunc function (Rsubread package) for feature counts
Scholar 3.3 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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