User: lhdcsu

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lhdcsu20
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Posts by lhdcsu

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Comment: C: Any tools to quantify intron retention in RNAseq data?
... whole genome. (tested on BAM from the STAR software) ...
written 12 months ago by lhdcsu20
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Answer: A: How to define the gene length for RPKM calculation
... Different types of gene lengths can be easily calculated using GTFtools:http://www.genemine.org/gtftools.php type 1: mean of lengths of isoforms. type 2: median of lengths of isoforms. type 3: max of lengths of isoforms. type 4: length of merged exons of isoforms. ...
written 13 months ago by lhdcsu20
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Answer: A: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... Recommend the GTFtools package at: http://www.genemine.org/gtftools.php. Using the '-l' options, four types of gene lengths will be calculated. One of them is the non-overlapping exon length (merge all exons of multiple isoforms of the same gene). ...
written 13 months ago by lhdcsu20
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Answer: A: Any tools to quantify intron retention in RNAseq data?
... Use iREAD (intron retention analysis and detector) specifically designed to quantify intron retention: http://www.genemine.org/iread.php ...
written 14 months ago by lhdcsu20

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