User: Wei Shi

gravatar for Wei Shi
Wei Shi2.9k
Reputation:
2,920
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Location:
Australia
Website:
http://www.wehi.edu.au...
Last seen:
4 hours ago
Joined:
11 years, 6 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 • 364 results • page 1 of 37 • next >
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... You commands look fine. I have no idea why you got no mapped reads at all. You may try to Blast some reads to all nucleotide databases to see if you could get any hits to other species: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome     ...
written 9 days ago by Wei Shi2.9k
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Comment: C: mapping FASTQ files to single gene (fluorescent reporter)
... As per the posting guide, you need to provide the session info so we can see what versions of software packages you use. Please also provide the full screen output of buildindex() and align() functions. How long are the two reference sequences? ...
written 13 days ago by Wei Shi2.9k
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Comment: C: Featurecounts issue for counting exons: Not matching total counts mapped for spe
... I would recommend you to merge the duplicated or overlapping exons. This is what flattenGTF function does. Output of this function is a data.frame object that contains a SAF format annotation. Take a look at the help page for flattenGTF for more information. You can then feed the data.frame object t ...
written 14 days ago by Wei Shi2.9k
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Answer: A: Featurecounts issue for counting exons: Not matching total counts mapped for spe
... Yes as you suspect there should be duplicates in the annotated exons for this gene. You can check this by looking at the exon annotation data featureCounts extracted from the GTF file (the extracted annotation is saved in the component fc$annotation). When you count reads at exon level, by default ...
written 15 days ago by Wei Shi2.9k
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Comment: C: Error while using buildindex for human genome
... The reason why most of your reads were not assigned to genes is because they do not overlap any genes (see the 'Unassigned_NoFeatures' category). This suggests that a lot of off-target reads were generated in your samples. ...
written 5 weeks ago by Wei Shi2.9k
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Answer: A: Rsubread for microbiome data analysis: genome >4GB
... Dear Evan, Yes Rsubread cannot build an index for the reference sequences containing more than 4 billion bases. You will have to break down your reference libraries into blocks each containing < 4 billion bases and then map your reads to each block separately. The buildindex() function adds a s ...
written 5 weeks ago by Wei Shi2.9k
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Comment: C: Error while using buildindex for human genome
... No worries Roopali. The featureCounts counting is not affected by the use of a full index or a gapped index. Could you please show the counting summary by running the following command? This will tell you the reasons why your reads were not counted. fc$stat   ...
written 5 weeks ago by Wei Shi2.9k
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Comment: C: Error while using buildindex for human genome
... Hi Roopali, the counts will be slightly different as the mapping results will be slightly different when using different types of indices. However this should have very little effect on the downstream analysis such as differential expression analysis. ...
written 6 weeks ago by Wei Shi2.9k
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Comment: C: Error while using buildindex for human genome
... The use of indexSplit=TRUE and memory=4000 significantly reduces the amount of memory used by buildindex for index building. With this setting, the index is split into multiple blocks (indexSplit=TRUE) and each block has a size no greater than 4000MB (memory=4000). Setting gappedIndex=TRUE allows a ...
written 7 weeks ago by Wei Shi2.9k
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Comment: C: Error while using buildindex for human genome
... Hi Roopali, could you also provide the screen output from buildindex? This function has been successfully tested on unix servers. Would you please run the following command on your Mac to see if it works? buildindex(basename="GRCh38",reference="GRCh38_latest_genomic.fna",gappedIndex=TRUE,indexSpli ...
written 7 weeks ago by Wei Shi2.9k

Latest awards to Wei Shi

Popular Question 6 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 6 months ago, created an answer that has been accepted. For A: featureCounts for multiple features
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: featureCounts for multiple features
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: File not found error when using dupRadar::analyzeDuprates
Scholar 17 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
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: Hisat2 vs featureCounts summary statistics
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Explainnation of featureCounts in-built annotation?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: nthreads option does NOT work in rsubread featureCounts
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Reads mistakenly being assigned to Unassigned_NoFeatures category when using fea
Popular Question 17 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 17 months ago, created an answer that has been accepted. For A: Low number of assigned reads using featureCounts / Strandedness issue
Scholar 17 months ago, created an answer that has been accepted. For A: Explainnation of featureCounts in-built annotation?
Popular Question 19 months ago, created a question with more than 1,000 views. For Experimental data package 'seqc'
Scholar 19 months ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Teacher 19 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 22 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Running featureCounts() in 'IntersectionStrict' mode
Scholar 2.7 years ago, created an answer that has been accepted. For A: Hisat2 vs featureCounts summary statistics
Scholar 2.7 years ago, created an answer that has been accepted. For A: featureCounts Parameters for Exon Junctions
Scholar 2.9 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 2.9 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 2.9 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?
Teacher 3.2 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 3.5 years ago, created an answer that has been accepted. For C: Are the endpoints included in intervals for SAF format?

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