User: Wei Shi

gravatar for Wei Shi
Wei Shi2.7k
Reputation:
2,710
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Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
17 hours ago
Joined:
10 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 • 317 results • page 1 of 32 • next >
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Answer: A: Rsubread counting peaks ATACseq
... Hi JB, I could not clearly see the peak names in your IGV figure but it seems your "Peak_3" overlaps with another peak, ie there is another peak in your SAF annotation that overlaps "Peak_3". featureCounts does not count reads that overlap more than one feature by default and this might be the reaso ...
written 7 days ago by Wei Shi2.7k
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Answer: A: Explainnation of featureCounts in-built annotation?
... Yes the annotations are for each exon, not for genes. You can work out the transcriptional start and end positions of genes by using the coordinates of exons belonging to the same gene and the strand information. An easier way might be to use the getInBuiltAnnotation function in Rsubread. This func ...
written 24 days ago by Wei Shi2.7k
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Job: Bioinformatics postdoc in Shi Lab at the Walter and Eliza Hall Institute, Melbourne, Australia
... An opportunity is available for a talented Research Officer to join the Shi Lab to work on the development of new bioinformatics methods and on the analyses of sequencing datasets. The appointee will work under the supervision of Dr Wei Shi and collaborate with Prof Axel Kallies’ group at the Peter ...
job bioinformatician job postdoc written 5 weeks ago by Wei Shi2.7k
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Comment: C: DIfferent mm10 gtf annotation files cause big difference in percentage of succes
... You got a lot more reads in category 'Unassigned_NoFeatures' when using Illumina GTF, which means that there is much less genes in this GTF overlapping with your reads. Did you use this GTF correctly? Both featureCounts inbuilt annotation and Illumina iGenomes annotation were based on RefSeq genes a ...
written 5 weeks ago by Wei Shi2.7k
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Comment: C: DIfferent mm10 gtf annotation files cause big difference in percentage of succes
... Could you provide the counting summary for each of your runs? It can be found in the stat component in the object returned by featureCounts. This will give you an idea on why less reads were counted with Illumina and Ensembl annotations. ...
written 6 weeks ago by Wei Shi2.7k
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Comment: C: Feature Count annotation file problem
... Hi, you need to follow the posting guide (http://www.bioconductor.org/help/support/posting-guide/) when you ask a question. For example, you need to provide information such as versions of software tools you use, your scripts related to your question etc. Regarding your featureCounts question, you ...
written 6 weeks ago by Wei Shi2.7k
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Answer: A: nthreads option does NOT work in rsubread featureCounts
... First you will need to check if more than one CPU core was used when you ran with multiple threads. You can run 'top' command under linux shell to see how many cpu cores you are using. Another possibility is that most of featureCounts running time was spent on reading in and decompressing your bam ...
written 12 weeks ago by Wei Shi2.7k • updated 12 weeks ago by Gordon Smyth32k
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Answer: A: Install Rsubread in win10, failed, how to proceed?
... You may run Rsubread on Linux Bash Shell on Windows 10. The Linux Bash Shell is a new feature Microsoft adds to Windows 10. We found Rsubread runs smoothly on this shell. ...
written 4 months ago by Wei Shi2.7k
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Answer: A: read count summed over exons is greater tham the gene-level read count using fea
... Hi Ina, this is not unexpected since exon-spanning reads (reads overlapping more than one exon) were counted more than once in your exon-level counting but they were counted only once in your gene-level counting. These reads should be counted more than once in your exon-level counting since they ori ...
written 5 months ago by Wei Shi2.7k
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Comment: C: problem running featurecounts using hg38 in-built annotation
... Hi Rich, could you please provide the complete output from your featureCounts run? Also you should update your copy of Rsubread and Bioc to their latest version as well. ...
written 5 months ago by Wei Shi2.7k

Latest awards to Wei Shi

Popular Question 6 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 6 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 6 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 9 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 19 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 19 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 19 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 21 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 21 months 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 22 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.1 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 2.4 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.5 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 3.0 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 3.0 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 3.0 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 3.2 years ago, created 100 posts.

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