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User: Wei Shi

gravatar for Wei Shi
Wei Shi3.0k
Reputation:
2,980
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
17 hours ago
Joined:
11 years, 8 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 • 368 results • page 1 of 37 • next >
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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 14 days 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 26 days 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 26 days 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 The version of Rsubread you use seems to be a outdated one.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 28 days 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 10 weeks ago by Wei Shi3.0k
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... As per the posting guide, you need to provide the session info so we can see what versions of software packages you use. Please also provide the full screen output of buildindex() and align() functions. How long are the two reference sequences? ...
written 10 weeks ago by Wei Shi3.0k
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Comment: C: Featurecounts issue for counting exons: Not matching total counts mapped for spe
... I would recommend you to merge the duplicated or overlapping exons. This is what flattenGTF function does. Output of this function is a data.frame object that contains a SAF format annotation. Take a look at the help page for flattenGTF for more information. You can then feed the data.frame object t ...
written 10 weeks ago by Wei Shi3.0k
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Answer: A: Featurecounts issue for counting exons: Not matching total counts mapped for spe
... Yes as you suspect there should be duplicates in the annotated exons for this gene. You can check this by looking at the exon annotation data featureCounts extracted from the GTF file (the extracted annotation is saved in the component fc$annotation). When you count reads at exon level, by default ...
written 11 weeks ago by Wei Shi3.0k
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Comment: C: Error while using buildindex for human genome
... The reason why most of your reads were not assigned to genes is because they do not overlap any genes (see the 'Unassigned_NoFeatures' category). This suggests that a lot of off-target reads were generated in your samples. ...
written 3 months ago by Wei Shi3.0k
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Answer: A: Rsubread for microbiome data analysis: genome >4GB
... Dear Evan, Yes Rsubread cannot build an index for the reference sequences containing more than 4 billion bases. You will have to break down your reference libraries into blocks each containing < 4 billion bases and then map your reads to each block separately. The buildindex() function adds a s ...
written 3 months ago by Wei Shi3.0k

Latest awards to Wei Shi

Popular Question 8 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 8 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 20 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 20 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 20 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 20 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 20 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 20 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 20 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 21 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 21 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 21 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 2.0 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.9 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.9 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.9 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 3.0 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.0 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 3.1 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 3.6 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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