User: Wei Shi

gravatar for Wei Shi
Wei Shi2.6k
Reputation:
2,610
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
6 days, 9 hours ago
Joined:
10 years 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 • 305 results • page 1 of 31 • next >
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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 13 days 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 27 days 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 weeks 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 8 weeks ago by Wei Shi2.6k
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Answer: A: Rsubread crash on Mac during alignment
... Dear Richard, thanks for sending us your data. This should be fixed it in the latest version (1.24.2) - it runs well on our Macbook. Wei ...
written 10 weeks ago by Wei Shi2.6k
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Comment: C: % of assigned reads using Rsubread featureCounts useMetaFeatures
... Hi @IV, I am not sure I understand your question. Could you please provide your code and also summary stat for each run? ...
written 11 weeks ago by Wei Shi2.6k
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Comment: C: Rsubread crash on Mac during alignment
... Dear Rich, could you please send us the fastq files under question so we can take a close look? Thanks, Wei ...
written 3 months ago by Wei Shi2.6k
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Comment: C: featureCounts creating fragments and high NoFeatures value
... Also you do not need to sort your bam files by position before you feed them to featureCounts. featureCounts accepts both name-sorted and location-sorted bam files. It processes these files in the same speed and returns you identical counting results. ...
written 3 months ago by Wei Shi2.6k
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Answer: A: featureCounts creating fragments and high NoFeatures value
... As @WouterDeCoster pointed, featureCounts counts alignments not reads. The total number of alignments will be greater than total number of reads if there are reads in your bam file that were reported multiple times. The reporting of multi-mapping reads may increase the number in every category in f ...
written 3 months ago by Wei Shi2.6k
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Comment: C: Variance between runs of Rsubread
... We aim to release it in the next few weeks. Cheers, Wei ...
written 4 months ago by Wei Shi2.6k

Latest awards to Wei Shi

Popular Question 18 days ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 27 days ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Autobiographer 3 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 13 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 13 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 13 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 15 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 15 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 16 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 23 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: Possible bug in Rsubread Phred-Score read
Scholar 2.0 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 2.5 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 2.5 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 2.5 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 A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 2.7 years ago, created 100 posts.

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