## User: Yang Liao

Yang Liao110
Reputation:
110
Status:
Trusted
Location:
Australia
Last seen:
2 weeks ago
Joined:
5 years, 10 months ago
Email:
l***@wehi.edu.au

#### Posts by Yang Liao

<prev • 15 results • page 1 of 2 • next >
1
258
views
1
... 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 7 weeks ago by Yang Liao110
1
258
views
1
... 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 8 weeks ago by Yang Liao110
1
75
views
1
... 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 10 weeks ago by Yang Liao110
0
188
views
0
... 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 4 months ago by Yang Liao110
0
188
views
0
... 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 4 months ago by Yang Liao110 • updated 4 months ago by Gordon Smyth37k
1
268
views
1
... 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 4 months ago by Yang Liao110
2
266
views
2
... 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 6 months ago by Yang Liao110
1
651
views
1
... 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 11 months ago by Yang Liao110
3
612
views
3
... 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 12 months ago by Yang Liao110
3
612
views
3
... 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 12 months ago by Yang Liao110

#### Latest awards to Yang Liao

Scholar 11 months ago, created an answer that has been accepted. For A: Error with featureCounts