User: Yang Liao

gravatar for Yang Liao
Yang Liao110
Reputation:
110
Status:
Trusted
Location:
Australia
Last seen:
4 hours ago
Joined:
5 years, 8 months ago
Email:
l***@wehi.edu.au

Posts by Yang Liao

<prev • 14 results • page 1 of 2 • next >
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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 2 days ago by Yang Liao110
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Answer: A: Index genome generation with Subread for colorspace data
... 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 15 days ago by Yang Liao110
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Comment: C: featureCounts error : SAM_pairer_iterate_tags
... 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 10 weeks ago by Yang Liao110
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Comment: C: featureCounts error : SAM_pairer_iterate_tags
... 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 11 weeks ago by Yang Liao110 • updated 11 weeks ago by Gordon Smyth37k
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Comment: C: Rsubread- feature counts
... 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 3 months ago by Yang Liao110
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Answer: C: GZIP ERROR:-2 using featureCounts (Subread)
... 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 5 months ago by Yang Liao110
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Comment: C: makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGen
... 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 9 months ago by Yang Liao110
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Comment: C: Rsubread install fails, "unable to load shared object Rsubread.so"
... Thanks for the detailed explanation! Yes, I can now reproduce the error by adding "-O 0" to the compiler parameters. It is a little surprising to see that an optimisation option can change the legitimate behaviour of the compiler. I have removed this keyword from my codes.  ...
written 10 months ago by Yang Liao110
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Answer: A: Rsubread install fails, "unable to load shared object Rsubread.so"
... I understand that the "inline" keyword instructs the compiler to embed the function into all its callers, and modern compilers are smarter to automatically make the decision, leaving this keyword obsolete. However, it should be harmless when you build a shared object from the codes including inline ...
written 10 months ago by Yang Liao110
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Comment: C: Rsubread featureCounts with byReadGroup
... Thanks! I've downloaded the data, and found that featureCounts had a bug in the routine for fixing the BAM format. It did not keep the read group names when fixing the BAM files from Picard or STAR.  This bug has been fixed. The next released version should work on your BAM files. Cheers, Yang ...
written 18 months ago by Yang Liao110

Latest awards to Yang Liao

Scholar 9 months ago, created an answer that has been accepted. For A: Error with featureCounts
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rsubread install fails, "unable to load shared object Rsubread.so"
Teacher 10 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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