**0**wrote:

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.

**24k**• written 26 days ago by danielryan9287 •

**0**