I ve aligned a list of sequence to a transcript to observe if this sequences are present in the transcript. I produced a BAM file. This is the result of my Alignement.
Left reads: Input : 27849344 Mapped : 16442 ( 0.1% of input) of these: 7259 (44.1%) have multiple alignments (56 have >100) Right reads: Input : 27849344 Mapped : 15211 ( 0.1% of input) of these: 8390 (55.2%) have multiple alignments (56 have >100) 0.1% overall read mapping rate. Aligned pairs: 5975 of these: 3776 (63.2%) have multiple alignments 194 ( 3.2%) are discordant alignments 0.0% concordant pair alignment rate. ~
Now I have to see that I don't count the same read twice, because I have changed the multiple alignment parameters. If a read maps on two different sequences, it is always the same read. I have to count the reads as unique. So how can I made this check?