User: Wei Shi

gravatar for Wei Shi
Wei Shi3.2k
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3,200
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Australia
Website:
http://www.wehi.edu.au...
Last seen:
15 hours ago
Joined:
12 years, 5 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 2 of 40 • next >
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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 4 months ago by Wei Shi3.2k
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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 5 months ago by Wei Shi3.2k
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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 5 months ago by Wei Shi3.2k
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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 5 months ago by Wei Shi3.2k
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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 months ago by Wei Shi3.2k • updated 6 months ago by Gordon Smyth39k
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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 6 months ago by Wei Shi3.2k
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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 6 months ago by Wei Shi3.2k
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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 6 months ago by Wei Shi3.2k
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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 7 months ago by Wei Shi3.2k
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Answer: A: featureCounts from RnaSeqGeneEdgeRQL returning a matrix of counts full of 0...
... First you don't need to modify your GFF file in order to run `featureCounts`. The command below should work for your original GFF file. fc <- featureCounts(all.bam, annot.ext="ThePathofMyGtfFile", isGTFAnnotationFile=TRUE, nthreads=16, GTF.featureType="gene", GTF.attrType="ID", allowMultiOve ...
written 7 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 3 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Supporter 10 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Popular Question 10 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 10 months ago, created a question with more than 1,000 views. For multiple hits with countOverlaps function
Guru 10 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
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: featureCounts for multiple features
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 2.4 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 2.4 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 2.4 years ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.4 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.4 years ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Popular Question 2.5 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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