User: Wei Shi

gravatar for Wei Shi
Wei Shi3.2k
Reputation:
3,200
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
18 hours ago
Joined:
12 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 • 391 results • page 1 of 40 • next >
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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 7 days 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 15 days 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 17 days 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 5 weeks 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 11 weeks 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 11 weeks 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 12 weeks 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 3 months ago by Wei Shi3.2k
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Answer: A: Can't run with gff3 file
... You did not use the `-F` option correctly - you need to provide a value to it. For your case, you can specify this option as `-F 'GTF'`. You actually do not need to specify this option at all as `'GTF'` is the default value. The `'GTF'` value denotes both `GTF` format and compatible `GFF` formats ...
written 3 months ago by Wei Shi3.2k
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Answer: A: Killed 9 on macOS Mojave for Rsubread buildindex
... To build a full index for human/mouse genome, `buildindex` function will need 15GB of memory. Mapping functions in Rsubread including `align` and `subjunc` will need 17.8GB of memory to perform read alignment using this full index. This enables fastest mapping speed, but it is recommended for use on ...
written 3 months ago by Wei Shi3.2k

Latest awards to Wei Shi

Popular Question 9 weeks ago, created a question with more than 1,000 views. For normalization of illumina bead array data
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
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
Supporter 9 months ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Popular Question 9 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 9 months ago, created a question with more than 1,000 views. For multiple hits with countOverlaps function
Guru 9 months ago, received more than 100 upvotes.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
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: featureCounts for multiple features
Teacher 16 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 2.3 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.3 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 2.3 years ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
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 2.3 years ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Scholar 2.3 years ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
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

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