User: Wei Shi

gravatar for Wei Shi
Wei Shi3.2k
Reputation:
3,200
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
2 hours ago
Joined:
12 years, 6 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 • 393 results • page 1 of 40 • next >
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Comment: C: featureCount error - cannot identify gene_id
... You can also try `flattenGTF` function in Rsubread to flatten exons. `flattenGTF` with `method="chop"` flattens exons in the same way as DEXSeq does. The default flattening method in `flattenGTF` is `merge`, which combines overlapping exons in the same gene to form a larger continous exon. This is ...
written 7 days ago by Wei Shi3.2k
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Comment: C: Error using Rsubread align: caugh segfault invalid permissions
... Your Rsubread version is not the latest. The latest version is 2.0.0. Your R is not up-to-date as well - the latest version is 3.6. ...
written 10 days ago by Wei Shi3.2k
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Answer: A: Replicating bowtie2 alignment parameters with Rsubread
... The `align` and `subjunc` functions in Rsubread always soft-clip reads if they find end bases in a read cannot be mapped, therefore they do not support the bowtie2 parameter '--end-to-end'. Rsubread aims to report confident mapping results for each base in each read. If end bases in a read can not b ...
written 8 weeks ago by Wei Shi3.2k
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Answer: C: Rsubread CIGAR output M only?
... This is something we will consider in the future development. But it is not supported at the moment. ...
written 10 weeks ago by Wei Shi3.2k
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Answer: A: "ERROR: cannot create temp file" when using buildindex from Rsubread
... Your working directory does not seem to be writable. `buildindex` needs to have write permission to the directory so it can write temporary files and output index files. ...
written 10 weeks ago by Wei Shi3.2k
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Answer: A: Collecting unmapped RNA-seq reads
... As Gordon said the Subread output includes both mapped and unmapped reads. It is fairly straightforward to extract unmapped reads from a SAM file. The '`RNAME`' column (the 3rd column) in the SAM file contains a value '`*`' for each unmapped read. ...
written 3 months ago by Wei Shi3.2k
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Answer: A: the coordinates of exons of RefSeq or ENSEMBL genes
... You can certainly use Bioc core packages to do so, but the `getInBuiltAnnotation` function in `Rsubread` offers you a simple way to get this information for human and mouse RefSeq genes. ...
written 4 months ago by Wei Shi3.2k
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Answer: A: Problem in featureCounts file.
... The records with more than one chr names contain genes that include multiple exons. `featureCounts` outputs chr name and coordinates for each exon in its count table. The `length` is however calculated for the whole gene, representing the total number of unique exonic bases included in a gene. ...
written 4 months ago by Wei Shi3.2k
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Comment: C: Error while using buildindex for human genome
... If you read the help page for `featureCounts` function, you will find that it returns the matrix table in the `counts` component of its returned object. ...
written 4 months ago by Wei Shi3.2k
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Answer: A: Rsubread, Error in featureCounts paired end
... As Gordon has replied it is better not to mix paired-end reads with single-end reads in the same file and it is really unnecessary to trim reads before mapping as read aligners will take care of this for you. However we have modified `featureCounts` to make it be able to process bam files with mixe ...
written 4 months ago by Wei Shi3.2k

Latest awards to Wei Shi

Popular Question 3 months ago, created a question with more than 1,000 views. For normalization of illumina bead array data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
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
Supporter 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Popular Question 11 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 11 months ago, created a question with more than 1,000 views. For multiple hits with countOverlaps function
Guru 11 months ago, received more than 100 upvotes.
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Popular Question 18 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 18 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 2.5 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
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 2.5 years ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 2.6 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea

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