User: Wei Shi

gravatar for Wei Shi
Wei Shi3.0k
Reputation:
3,020
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
1 week, 4 days ago
Joined:
11 years, 11 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 • 373 results • page 1 of 38 • next >
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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 12 days ago by Wei Shi3.0k
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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 12 days ago by Wei Shi3.0k
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Comment: C: featurecounts Rsubread ERROR on exon_id
... There is an attribute type `exonid` in the few annotation lines you provided but not 'exon\_id'. `featureCounts` from any previous versions of Rsubread releases won't work on 'exon\_id'. `featureCounts` also reported in its error message that the 9th column of the first CDS feature in your annotati ...
written 14 days ago by Wei Shi3.0k
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Comment: C: featurecounts Rsubread ERROR on exon_id
... As I mentioned in my reply `exon_ids` is not an attribute included in your annotation, so you should not use it in any parameters you provided to `featureCounts`. ...
written 15 days ago by Wei Shi3.0k
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Answer: A: featurecounts Rsubread ERROR on exon_id
... The error message tells you that 'exonid' is not a valid attribute and this resulted in the termination of `featureCounts`. You should use `geneid` instead for your exon-level counting. Also you should specify `useMetaFeatures=FALSE` so that the counting is performed at the feature level (ie exon le ...
written 18 days ago by Wei Shi3.0k
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Answer: A: The optimal minMQS parameter in featureCounts for RNA-Seq quantification
... Please post your questions regarding Rsubread (featureCounts is part of it) to this Support Site as Rsubread is a Bioconductor package. In general I don't recommend throwing away reads with low MAQ value when you count them to genes. This is because an RNA-seq read with low MAQ is likely to be corr ...
written 11 weeks ago by Wei Shi3.0k
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Answer: A: How to change stringtie gene_id names with ref_gene_id when performing featureCo
... If "refgeneid" is included as an attribute type in your GTF file, you can set GTF.attrType="refgeneid" to instruct featureCounts to count reads to this type of genes. The parameter "GTF.attrType.extra" does not work for this purpose. It just extracts extra annotation data from your gtf file and add ...
written 12 weeks ago by Wei Shi3.0k
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Comment: C: Rsubread- feature counts
... As I mentioned in my answer above, the value you provided to the 'annot.ext' parameter is invalid. It does not contain a file name. You need to make sure the file path is correct and a file name is provided. ...
written 12 weeks ago by Wei Shi3.0k
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Answer: C: Rsubread- feature counts
... The version of Rsubread you use seems to be a outdated one. Please update it to the latest version. The first error has been fixed in latest versions. Also you did not provide a valid annotation file for the 'annot.ext' parameter. ...
written 3 months ago by Wei Shi3.0k
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... You commands look fine. I have no idea why you got no mapped reads at all. You may try to Blast some reads to all nucleotide databases to see if you could get any hits to other species: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome     ...
written 4 months ago by Wei Shi3.0k

Latest awards to Wei Shi

Popular Question 10 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 10 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 22 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 22 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 22 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 22 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 22 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 22 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 22 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 23 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: Running featureCounts() in 'IntersectionStrict' mode
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
Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.0 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 3.0 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 3.0 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 3.2 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.2 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 3.3 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.5 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 3.8 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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