Hello everybody. I'm a Master Student in Molecular Biology and Bioinformatics and pretty new to NGS technologies. I am using bowtie2 in pair-end mode after using bowtie1 in single end mode on some nanoCAGE RNA seq data. The reason I'm doing this is because bowtie1 in pair end mode has less customizable options than bowtie2 and is not possible to choose the size for the alignment window for the pair end mates, so I had very low alignment score against my reference genome (between 12 and 14% against my 90% and over in single end mode).
I cannot understand the report of the alignment score of Bowtie 2 in some parts. Here's an example:
I have run bowtie 2 in pair end mode using the
option for the orientation of my reads.
according to the bolded part of the report, i have a lot of reads take in PE (because it specifies 6699600 mates out of 3349800 pairs which aligns nor concordantly nor discordantly (so they are not aligned on the genome). But still a fraction of these mates aligns. How is that possible? They shouldn't align at all!
also, I do not understand the overall score; Is there a place in which I can look to the criteria of this score? How does that 88.21% comes from?
Thanks for any kind of answer that you can give to me!
Daniele
I cannot understand the report of the alignment score of Bowtie 2 in some parts. Here's an example:
16182999 reads; of these:
16182999 (100.00%) were paired; of these:
5731231 (35.42%) aligned concordantly 0 times
4522376 (27.95%) aligned concordantly exactly 1 time
5929392 (36.64%) aligned concordantly >1 times
----
5731231 pairs aligned concordantly 0 times; of these:
2381431 (41.55%) aligned discordantly 1 time
----
3349800 pairs aligned 0 times concordantly or discordantly; of these:
6699600 mates make up the pairs; of these:
3814736 (56.94%) aligned 0 times
1883429 (28.11%) aligned exactly 1 time
1001435 (14.95%) aligned >1 times
88.21% overall alignment rate
16182999 (100.00%) were paired; of these:
5731231 (35.42%) aligned concordantly 0 times
4522376 (27.95%) aligned concordantly exactly 1 time
5929392 (36.64%) aligned concordantly >1 times
----
5731231 pairs aligned concordantly 0 times; of these:
2381431 (41.55%) aligned discordantly 1 time
----
3349800 pairs aligned 0 times concordantly or discordantly; of these:
6699600 mates make up the pairs; of these:
3814736 (56.94%) aligned 0 times
1883429 (28.11%) aligned exactly 1 time
1001435 (14.95%) aligned >1 times
88.21% overall alignment rate
I have run bowtie 2 in pair end mode using the
Code:
-fr
according to the bolded part of the report, i have a lot of reads take in PE (because it specifies 6699600 mates out of 3349800 pairs which aligns nor concordantly nor discordantly (so they are not aligned on the genome). But still a fraction of these mates aligns. How is that possible? They shouldn't align at all!
also, I do not understand the overall score; Is there a place in which I can look to the criteria of this score? How does that 88.21% comes from?
Thanks for any kind of answer that you can give to me!
Daniele
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