User: Wei Shi

gravatar for Wei Shi
Wei Shi2.6k
Reputation:
2,640
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
20 hours ago
Joined:
10 years, 4 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 • 311 results • page 1 of 32 • next >
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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 28 days ago by Wei Shi2.6k • updated 28 days ago by Gordon Smyth31k
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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 11 weeks ago by Wei Shi2.6k
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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 3 months ago by Wei Shi2.6k
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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 3 months ago by Wei Shi2.6k
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Answer: A: Using Rsubread with FASTA sequence files over 4 GB
... Hi Bryan, as shown in the error message Rsubread cannot build an index for a reference genome that includes more than 4 gigabases. You will have to split the genome into two or more pieces before you can build index and perform mapping. ...
written 3 months ago by Wei Shi2.6k
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Comment: C: Rsubread crash on Mac during alignment
... Thanks for letting us know Rich! ...
written 3 months ago by Wei Shi2.6k
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Comment: C: FeatureCounts output to SAM like htseq-counts?
... This is something we are currently working on. Will try to add this feature soon. ...
written 4 months ago by Wei Shi2.6k
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Answer: A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
... Your command requires each read to 100% overlap with a feature ('--fracOverlap 1') but the reads you provided do not 100% overlap with any feature. These reads have soft-clipped bases ('S' section in CIGAR) or inserted bases ('I' section in CIGAR), making them have the fraction of overlapping bases ...
written 4 months ago by Wei Shi2.6k
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Comment: C: FeatureCounts --read2pos option
... Apologies for my late response. This refers to both GFF and SAF annotations. ...
written 5 months ago by Wei Shi2.6k
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Answer: A: FeatureCounts --read2pos option
... One way to get around this is to change your annotation - subtracting/adding each P-site coordinate by 12 (depending on which strand the P-site is on). In the meantime, we are working on letting read2pos parameter work with readExtension5 parameter (and readExtension3 parameter) to reduce the read ...
written 6 months ago by Wei Shi2.6k

Latest awards to Wei Shi

Popular Question 4 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 4 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 4 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 7 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 17 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 17 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 17 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 19 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 19 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 20 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 23 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 2.2 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.3 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 2.9 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 2.9 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.9 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 3.0 years ago, created 100 posts.

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