## User: Yang Liao

Yang Liao110
Reputation:
110
Status:
Trusted
Location:
Australia
Last seen:
1 week, 3 days ago
Joined:
6 years, 1 month ago
Email:
l***@wehi.edu.au

#### Posts by Yang Liao

<prev • 17 results • page 1 of 2 • next >
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... 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 11 days ago by Yang Liao110
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... 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 12 days ago by Yang Liao110
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... 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 4 months ago by Yang Liao110
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... 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 4 months ago by Yang Liao110
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... Hi Gökberk, I downloaded the 5.0 version of the Macaca Fascicularis genome from Ensembl (the top-level sequences, 867 MB in gzipped format). I then ran the index builder in Subread-1.6.4 with the same arguments as you used. The index was built in 45 minutes with no error, and the "scan uninformativ ...
written 5 months ago by Yang Liao110
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... Thanks, Leo. I've received the BAM file, and featureCounts (v.1.6.3) ran smoothly on it, with the read-count table generated. I've sent you some further suggestions to try, and if everything just doesn't work, I hope to build a special version of featureCounts with running details written into logs, ...
written 7 months ago by Yang Liao110
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... From the error message in your post, it is a "general format error" encountered by featureCounts. In other words, featureCounts couldn't correctly parse the current alignment record in the BAM file. I generated a BAM file myself using rsem-tbam2bgam` but featureCounts ran correctly on it. Can you ...
written 7 months ago by Yang Liao110 • updated 7 months ago by Gordon Smyth38k
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... Thanks for the details. I noticed that you ran propmapped() on the BAM files, then gave the return value from propmapped() directly to featureCounts(). As you may have noticed, the return value from propmapped() is a data.frame object, and featureCounts cannot take a data.frame as the argument for i ...
written 7 months ago by Yang Liao110
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... Hi Gwenael, The "GZIP ERROR:-2" message sounds like an old bug in featureCounts. Which version of featureCounts did you use? If it was not the latest version (v1.6.3), you can try our latest version, which is available on   https://sourceforge.net/projects/subread/files/subread-1.6.3/ since this ...
written 9 months ago by Yang Liao110
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... I'm facing the same problem and I found that the makeTxDbFromGFF() function already dropped the exons if they span multiple chromosomes and/or multiple strands. I built a GTF file that contains only four exons from one gene, but from different strands of chr1. The makeTxDbFromGFF() function gave wa ...
written 14 months ago by Yang Liao110

#### Latest awards to Yang Liao

Scholar 14 months ago, created an answer that has been accepted. For A: Error with featureCounts