User: dbpzdbpz

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dbpzdbpz100
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Australia
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1 year, 1 month ago
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Posts by dbpzdbpz

<prev • 9 results • page 1 of 1 • next >
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Answer: A: FeatureCounts summarizing at exon level
... The "-B" option is not necessary for exon-level counting, but it can improve (maybe very little) the accuracy of analysis by not considering the read-pairs that are suspiciously low-quality. The "-O" option is not necessary if your aligner is not junction-aware, namely they don't report the exon-ex ...
written 15 months ago by dbpzdbpz100
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Answer: A: Creating SAF data table for featureCounts for viral RNA-Seq
... The "Chr" values in the annotations for featureCounts don't need to be chromosome names. They can be contig names or anything as long as the names coincide with the chromosome names in your SAM or BAM files (in the @SQ header lines and also the third column of the alignment results). In your case, ...
written 15 months ago by dbpzdbpz100
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Answer: A: featureCounts duplicate counting
... When you specified "--ignoreDup", featureCounts will test the FLAGS field in the SAM/BAM file to see if it is a duplicated mapping. In particular, the bit in the FLAGS being tested is 0x400 (1024). This bit is set by the aligner according to its own strategy. Based on the summarization information ...
written 5.1 years ago by dbpzdbpz100
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Answer: A: Intron level featureCounts gives segfault
... Sorry for the segmentation faults. There were two bugs in the old version of featureCounts in R that were related to the annotation files and were able to crash the R session. These two bugs have been fixed in the new Rsubread package. The new package is available on BioC 2.14. The version of the n ...
written 5.2 years ago by dbpzdbpz100
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Comment: C: how to use a bed file with htseq-count
... Sorry that there were two annotation-related bugs in the old featureCounts-1.4.4 version that can crash the program. We have fixed the bugs and made a new release (1.4.5) yesterday:     http://sourceforge.net/projects/subread/files/subread-1.4.5/  Can you please try the new version? I hope it can ...
written 5.3 years ago by dbpzdbpz100
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Comment: C: Remove duplicates in featurecounts
... Sorry that it was delayed for weeks. The 1.4.5 version of subread (inc. featureCounts) was released yesterday on sf.net. http://sourceforge.net/projects/subread/ ...
written 5.3 years ago by dbpzdbpz100
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Answer: A: Remove duplicates in featurecounts
... The new version of subread (1.4.5) will provide a function to ignore reads or fragments that have the 0x400 flag (the duplicate read flag). This version should be released in days. ...
written 5.3 years ago by dbpzdbpz100
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Answer: A: Compariosn Htseq And Feature Count
... I think it is interesting to compare the two programs. FeatureCounts runs much faster and supports more input formats (including BAM files that are sorted by either read names or genomic coordinates). But it is also important to compare the read assignment results after all. For single-end reads, t ...
written 5.5 years ago by dbpzdbpz100
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Answer: A: What Does Requirebothendsmapped From Rsubread Package Means?
... Dear Roll, Thank you for using featureCounts. If you set "requireBothEndsMapped" to TRUE, featureCount ignores the read pairs (i.e., fragments) that have only one end mapped, but the other end unmapped. Generally speaking, requiring both ends to be mapped reduces sensitivity but improves specifici ...
written 5.6 years ago by dbpzdbpz100

Latest awards to dbpzdbpz

Scholar 15 months ago, created an answer that has been accepted. For A: featureCounts duplicate counting
Scholar 5.1 years ago, created an answer that has been accepted. For A: featureCounts duplicate counting

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