User: Wei Shi

gravatar for Wei Shi
Wei Shi2.6k
Reputation:
2,580
Status:
Trusted
Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
2 hours ago
Joined:
9 years, 10 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 • 301 results • page 1 of 31 • next >
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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 7 days 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 17 days 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 6 weeks 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 7 weeks 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 7 weeks 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 9 weeks ago by Wei Shi2.6k
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Comment: C: Variance between runs of Rsubread
... Hi Isaac, this will be fixed in the next version which should be released soon. ...
written 9 weeks ago by Wei Shi2.6k
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Comment: C: Variance between runs of Rsubread
... Yes we have downloaded the files. Thanks. ...
written 4 months ago by Wei Shi2.6k
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Answer: A: featureCounts Parameters for Exon Junctions
... featureCounts uses GTF.featureType and GTF.attrType parameters to get meta features (eg. genes) and the features belonging to the same meta feature. It then uses the feature coordinates to work out the start and end locations of each meta feature. A junction is assigned to a meta feature if its dono ...
written 4 months ago by Wei Shi2.6k
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Answer: A: Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
... The buildindex() function uses separators including "|", " " and <TAB> to divide the name of a reference sequence into multiple substrings and then it uses the first substring to represent this reference sequence. As more than one of your reference sequences have name starting with "gi|", you ...
written 4 months ago by Wei Shi2.6k

Latest awards to Wei Shi

Autobiographer 5 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 11 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 11 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 11 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 C: Are the endpoints included in intervals for SAF format?
Teacher 13 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 14 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 17 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 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: Possible bug in Rsubread Phred-Score read
Scholar 22 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Appreciated 2.4 years ago, created a post with more than 5 votes. For Experimental data package 'seqc'
Scholar 2.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 2.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 2.5 years ago, created 100 posts.

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