Hi all , I am using bowtie2 for mapping illumina paired end mapping. Is there any option for getting the reads which are aligned neither concordantly nor dicordantly? All my reads have pairs. From the manual I infered that --un-conc can be used to get the paired end reads which are failed to align concordantly.
In paired end read alignment whether we have to completely ignore the discordant reads? How much importance we have to give the discordant reads?
Following is the sample of my bowtie2 status summary:
465909 reads; of these:
465909 (100.00%) were paired; of these:
61524 (13.21%) aligned concordantly 0 times 322977 (69.32%) aligned concordantly exactly 1 time 81408 (17.47%) aligned concordantly >1 times ---- 61524 pairs aligned concordantly 0 times; of these: 9488 (15.42%) aligned discordantly 1 time ---- 52036 pairs aligned 0 times concordantly or discordantly; of these: 104072 mates make up the pairs; of these: 67801 (65.15%) aligned 0 times 16898 (16.24%) aligned exactly 1 time (Question:If these pairs are aligned 0 times concordantly or discordantly, then in what way they are aligned? ) 19373 (18.61%) aligned >1 times
92.72% overall alignment rate