User: Wei Shi

gravatar for Wei Shi
Wei Shi3.1k
Reputation:
3,150
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
3 hours ago
Joined:
12 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 • 387 results • page 1 of 39 • next >
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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 20 days ago by Wei Shi3.1k
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63
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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 21 days ago by Wei Shi3.1k
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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 weeks ago by Wei Shi3.1k
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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 weeks ago by Wei Shi3.1k
1
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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 5 weeks ago by Wei Shi3.1k
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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 8 weeks ago by Wei Shi3.1k
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Answer: A: Killed 9 on macOS Mojave for Rsubread buildindex
... Your index building process was likely to be terminated by the system due to large amount of memory used by `buildindex` for building a full index for human genome. You may use the following command to build a gapped index to save memory. This will result in an increase in read mapping time but it ...
written 9 weeks ago by Wei Shi3.1k
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Comment: C: Is possible to use NOISeq with counts from RSubread?
... TopHat is a read aligner and it does not produce read counts. If you want to get read counts for genes you can use `featureCounts` function in Rsubread. The index you mentioned in Rsubread is used by `align` and `subjunc` for read mapping and I don't think NOISeq uses this index. So what is the 'cou ...
written 10 weeks ago by Wei Shi3.1k
1
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Answer: A: Boxplot function not showing all reads length on x-axis
... The problem is caused by the truncation of columns when `qualityScores` reads in the Phred score file generated by the C code. The number of columns in the returned score matrix is incorrectly determined by length of the first read in the fastq file, leading to longer reads being truncated. We will ...
written 10 weeks ago by Wei Shi3.1k
1
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Comment: C: Boxplot function not showing all reads length on x-axis
... By default, `qualityScores` extracts quality scores from 10000 reads in a fastq file. You can let `qualityScores` to extract quality scores from all reads in your fastq file by setting `nreads=105191`, to see if more base positions will be shown in your boxplot. QS <- qualityScores("pathofm ...
written 11 weeks ago by Wei Shi3.1k

Latest awards to Wei Shi

Scholar 20 days ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Popular Question 7 months ago, created a question with more than 1,000 views. For multiple hits with countOverlaps function
Guru 7 months ago, received more than 100 upvotes.
Scholar 7 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Popular Question 7 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Supporter 7 months ago, voted at least 25 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Popular Question 14 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 14 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 14 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 2.2 years ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 2.2 years ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
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: Hisat2 vs featureCounts summary statistics
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 2.2 years 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 2.3 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
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
Autobiographer 2.5 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.4 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics

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