Hello, I have trimmed by paired end data RNA seq (Illumina Miseq) data using trimmomatic. However after aligning with bowtie2, I get virtually noalignments. Please see below:
6953839 reads; of these: 6953839 (100.00%) were paired; of these: 6951481 (99.97%) aligned concordantly 0 times 2357 (0.03%) aligned concordantly exactly 1 time 1 (0.00%) aligned concordantly >1 times ---- 6951481 pairs aligned concordantly 0 times; of these: 38758 (0.56%) aligned discordantly 1 time ---- 6912723 pairs aligned 0 times concordantly or discordantly; of these: 13825446 mates make up the pairs; of these: 13825088 (100.00%) aligned 0 times 196 (0.00%) aligned exactly 1 time 162 (0.00%) aligned >1 times 0.59% overall alignment rate
However if I perform the alignment of the original fastq files (not trimmed), I get high alignments. See below:
7656360 reads; of these: 7656360 (100.00%) were paired; of these: 1097101 (14.33%) aligned concordantly 0 times 6195514 (80.92%) aligned concordantly exactly 1 time 363745 (4.75%) aligned concordantly >1 times ---- 1097101 pairs aligned concordantly 0 times; of these: 295377 (26.92%) aligned discordantly 1 time ---- 801724 pairs aligned 0 times concordantly or discordantly; of these: 1603448 mates make up the pairs; of these: 1203571 (75.06%) aligned 0 times 351300 (21.91%) aligned exactly 1 time 48577 (3.03%) aligned >1 times 92.14% overall alignment rate
Please let me know a possible reason for this?
Thanks.
