User: Wei Shi

gravatar for Wei Shi
Wei Shi2.7k
Reputation:
2,710
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
2 weeks, 2 days ago
Joined:
10 years, 9 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 • 322 results • page 1 of 33 • next >
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Comment: C: Rsubread Read Bam and filter reads by TAG field
... Sorry for my slow response. However I am not quite sure what feature you request here. As far as I know reads from each single cell are often organized as a read group in a bam file. Is the 'byReadGroup' option in featureCounts what you are after? ...
written 24 days ago by Wei Shi2.7k
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Comment: C: caught segfault when using featureCounts
... This is now fixed in both release and devel versions. ...
written 5 weeks ago by Wei Shi2.7k
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Comment: C: caught segfault when using featureCounts
... Thanks. We can reproduce the problem you encountered from our end. We found this was caused by a bug in the program that was related to the processing of bam files processed by Picard. We will release a fix soon. ...
written 5 weeks ago by Wei Shi2.7k
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Comment: C: caught segfault when using featureCounts
... Please do not run repair function on single-end reads since it is designed for processing paired-end reads. Could you provide an example of reads that were 'wrongly' sorted by repair? ...
written 9 weeks ago by Wei Shi2.7k
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Comment: C: caught segfault when using featureCounts
... Please follow the posting guide (http://www.bioconductor.org/help/support/posting-guide/) when you post a question. Provide output of sessionInfo() so we can know what versions of software packages you use. You also need to show the errors you got from running featureCounts. It will be best to provi ...
written 9 weeks ago by Wei Shi2.7k
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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 3 months 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 3 months 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 4 months 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 4 months 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 4 months ago by Wei Shi2.7k

Latest awards to Wei Shi

Popular Question 9 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 9 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 9 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 12 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 22 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
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: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.1 years 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 2.1 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: Use BAM file created from subjunc function (Rsubread package) for feature counts
Scholar 2.7 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.8 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 3.3 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 3.3 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 3.3 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.3 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 3.3 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 3.5 years ago, created 100 posts.

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