meaning of exon span juntion

Question

[GHanumanth404]

Can any one help me to understand what is the meaning of span exon junction?

Answer 1

[Brian Bushnell]

"Span Exon Junction" implies the presence of reads with one end mapping to one exon, and the other end mapping to another exon, thus spanning the intermediate intron. Can you rephrase the question, with more context?

[GHanumanth404]

actaully i am learining some basics of NGS data analysis . In one of the paper it says there is problem of analysing short reads bcoz they contain span exon junction. This are difficult to analyse

[Brian Bushnell]

If you want to contribute to this forum and receive thoughtful answers, please put in the effort to write grammatically and syntactically correct sentences.

[GHanumanth404]

ok!! Now can you give me answer ? In one of the paper it was reported that there is problem of analysing short read because they contain span exon junction. Why it is difficult to analyse such span exon junction

[WouterDeCoster]

Span is a verb. The read spans an exon junction, meaning that it is derived from two exons, meaning that it's not mapping in one location in the genome but will be a 'split read'. Depending on the length of the read and it's parts, this is a challenge for (correctly) aligning it to the genome.

[GHanumanth404]

ohh okay thanks WouterDeCoster

Answer 2

[GHanumanth404]

what is impact of RPKM FPKM TPM and CPM values? what is the difference in all and which should be prefered for RNA abundance??

[WouterDeCoster]

Please open a separate thread for a new question