quantification of bowtie2 output
Dear all, If we run Bowtie2 at default parameters then who do we know that how many parameters it included actually. through which we can correlate our mapping results. one more thing if we got 20% aligned exactly one time and suppose 16% align more than one times, If I would quantify this, each reads of 20% data UNIQUELY COMPLETELY [uniquely means each reads would be mapped exactly one coordinate of particular chromosome and completely means if read length is 100nts then total 100 nts would be align in continues manner (?)] [is it explainable further??? ]
if we talk about 16% of reads which aligned more than one position, there may be several possibilities: 1. few reads may be overloaded with 20% of reads which are mapped exactly ONE time. 2nd possibility, fraction of a read map different different location with unknown insert size. [any other possibility]
how could I get depth of reads which fall on a particular location of chromosome? what is the maximum occurrence reads adhering at same position at particular chromosomal location? in next step, apart from SAM tool is any other way for downstream analysis ???
if we talk about 16% of reads which aligned more than one position, there may be several possibilities: 1. few reads may be overloaded with 20% of reads which are mapped exactly ONE time. 2nd possibility, fraction of a read map different different location with unknown insert size. [any other possibility]
how could I get depth of reads which fall on a particular location of chromosome? what is the maximum occurrence reads adhering at same position at particular chromosomal location? in next step, apart from SAM tool is any other way for downstream analysis ???