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:
17 hours ago
Joined:
9 years, 11 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 • 303 results • page 1 of 31 • next >
0
votes
1
answers
109
views
1
answers
Comment: C: FeatureCounts --read2pos option
... Apologies for my late response. This refers to both GFF and SAF annotations. ...
written 5 days ago by Wei Shi2.6k
0
votes
1
answers
109
views
1
answers
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 27 days ago by Wei Shi2.6k
0
votes
2
answers
168
views
2
answers
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 5 weeks ago by Wei Shi2.6k
0
votes
0
answers
62
views
0
answers
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 6 weeks ago by Wei Shi2.6k
0
votes
2
answers
168
views
2
answers
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 10 weeks ago by Wei Shi2.6k
0
votes
2
answers
178
views
2
answers
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 11 weeks ago by Wei Shi2.6k
0
votes
2
answers
178
views
2
answers
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 11 weeks ago by Wei Shi2.6k
0
votes
1
answers
285
views
1
answers
Comment: C: Variance between runs of Rsubread
... We aim to release it in the next few weeks. Cheers, Wei ...
written 3 months ago by Wei Shi2.6k
0
votes
1
answers
285
views
1
answers
Comment: C: Variance between runs of Rsubread
... Hi Isaac, this will be fixed in the next version which should be released soon. ...
written 3 months ago by Wei Shi2.6k
0
votes
1
answers
285
views
1
answers
Comment: C: Variance between runs of Rsubread
... Yes we have downloaded the files. Thanks. ...
written 5 months ago by Wei Shi2.6k

Latest awards to Wei Shi

Autobiographer 9 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 12 months ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 12 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 12 months ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 14 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 14 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 15 months ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 18 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 22 months ago, created an answer with at least 3 up-votes. For A: Possible bug in Rsubread Phred-Score read
Scholar 23 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 2.5 years ago, created an answer that has been accepted. For A: Please, could someone help me to export featureCounts (Rsubread) results?
Centurion 2.6 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 299 users visited in the last hour