User: Wei Shi

gravatar for Wei Shi
Wei Shi3.1k
Reputation:
3,090
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Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
13 hours ago
Joined:
12 years 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 • 382 results • page 1 of 39 • next >
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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 13 hours 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 5 days 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 11 days ago by Wei Shi3.1k
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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 17 days ago by Wei Shi3.1k
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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 19 days ago by Wei Shi3.1k
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Answer: A: How to read Illumina data used in the MACQ project (GSE5350)
... The MAQC Illumina microarray data deposited on GEO do not have the original format. So the default parameter values of `read.ilmn` function won't work. Below is an example command to read in one of the files: ``` library(limma) x <- read.ilmn("ILM_1_A1.txt",probeid="TargetID",expr="ILM_") ``` ...
written 6 weeks ago by Wei Shi3.1k • updated 6 weeks ago by Gordon Smyth37k
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Answer: A: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... The problem you encountered with your read counting is due to the strand-specific counting of your singleton reads. You cannot perform a correct strand-specific counting for these reads because featureCounts does not know if they are the first read or the second read in a pair. If they are the first ...
written 7 weeks ago by Wei Shi3.1k
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Answer: A: Improving the performance of the align function from Rsubread for old Roche454 r
... Your mapping percentages sound reasonable to me. You will expect typically 80 percent or higher mapping rate for Illumina reads. But the 454 reads definitely have a lower mapping rate. Other than the reasons mentioned by @thokall, higher sequencing error rate (particularly indel errors) is another f ...
written 8 weeks ago by Wei Shi3.1k
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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... featureCounts can correctly process any bam files generated from the mapping of reads generated from a paired end library including those bam files that contain read pairs that have only one end mapped (the other end is not required to be included in the same file), as long as all the reads are mark ...
written 8 weeks ago by Wei Shi3.1k
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Answer: A: featureCounts for ATAC-seq
... I don't know what are the transposition events you are looking for. But if you are looking for the cleavage sites in the open chromatin regions, you can use the start position of reads to search such sites. The `--read2pos 5` option in `featureCounts` can help you to achieve this. The shifting and ...
written 10 weeks ago by Wei Shi3.1k

Latest awards to Wei Shi

Popular Question 12 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 12 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 24 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 24 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 24 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 24 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 24 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 24 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 24 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 2.1 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.1 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 2.4 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.2 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 3.2 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 3.2 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 3.4 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.4 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 3.4 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.7 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 4.0 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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