User: Yang Liao

gravatar for Yang Liao
Yang Liao180
Reputation:
180
Status:
Trusted
Location:
Australia
Last seen:
4 hours ago
Joined:
6 years, 3 months ago
Email:
l***@wehi.edu.au

Posts by Yang Liao

<prev • 23 results • page 1 of 3 • next >
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Answer: A: Rsubread malloc(): memory corruption
... I found that the very many "malloc" calls in the index builder make the heap of the R session a bit messy -- nearly every memory page contains allocated and not-allocated blocks. On a computer that has a huge amount of memory, there are still enough non-contaminated memory pages, but on a computer t ...
written 19 days ago by Yang Liao180
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Comment: C: Rsubread malloc(): memory corruption
... Sorry for the late response -- I now have an environment to reproduce the error. I found that Ubuntu 16.04 doesn't have this problem but Ubuntu 18.04 has it. It looks like R didn't actually release the memory allocated in the index-building step, although the index builder itself has called the mem ...
written 21 days ago by Yang Liao180
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Comment: C: Rsubread requests longread mode for shotgun RNAseq data
... Glad to know that the quick fix works for you. ...
written 4 weeks ago by Yang Liao180
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Answer: A: Rsubread requests longread mode for shotgun RNAseq data
... Hi Christian, I received the BAM file that you provided. Although the read sequences are short (76bp or so), there are some very long optional fields in many alignments. For example, read "HWI-ST700660:106:C0APYACXX:6:2206:5447:137301" has an optional field, "XA:Z", longer than 100,000 bytes. It i ...
written 5 weeks ago by Yang Liao180
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Comment: C: Rsubread requests longread mode for shotgun RNAseq data
... Hi Christian, Can you share your BAM file, please? I hope to look into the BAM file to see what was the cause of the error message. You can send the link to liao (AT) wehi.edu.au Thanks. Cheers, Yang ...
written 6 weeks ago by Yang Liao180
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Answer: A: Install Rsubread in win10, failed, how to proceed?
... Hi Yisong, The Rsubread package now supports Windows (64-bit) platforms. This includes the 64-bit Windows 10. Please follow the instructions on https://bioconductor.org/packages/release/bioc/html/Rsubread.html to install Rsubread on a Windows (64-bit) computer. It is recommended to run Rsubrea ...
written 7 weeks ago by Yang Liao180
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Comment: C: Rsubread malloc(): memory corruption
... Thanks for sharing the data. I used your fastq file, and used the same reference genome fasta file and the same annotation gtf file (the latter two files were downloaded from GENCODE). I also used your command lines. Rsubread_1.34.6 did index building and read mapping smoothly; around 95.5% reads w ...
written 9 weeks ago by Yang Liao180
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Comment: C: Rsubread malloc(): memory corruption
... What is the configuration of the host computer running the virtual machine? Say, is it a Windows computer or a Linux computer, and what virtual machine software was used? How much physical memory was available on the host computer? Could you share the input fastq file and the reference genome used ...
written 9 weeks ago by Yang Liao180
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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... One reason for featureCounts not allowing the mixture of single-end and paired-end reads in one SAM/BAM file is that the counts of single reads shouldn't be added to the counts of fragments because they are different things. A normal read aligner reports unpaired read mapping results as paired-end ...
written 6 months ago by Yang Liao180
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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... Hi Kristoffer, I'm not sure what is in the `paired_and_unpaired.bam` file. Does it contain both single-end and paired-end reads? You can figure it out by running `$ samtools view paired_and_unpaired.bam | awk 'and($2, 1) == 1' | wc -l` and `$ samtools view paired_and_unpaired.bam | awk 'and($2, ...
written 6 months ago by Yang Liao180

Latest awards to Yang Liao

Scholar 16 months ago, created an answer that has been accepted. For A: Error with featureCounts
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Rsubread install fails, "unable to load shared object Rsubread.so"
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Rsubread install fails, "unable to load shared object Rsubread.so"

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