bowtie2 summary looks very weird. Neither concordant nor discordant.

Question

[zhangzhenyusz]

Hi everybody,

My bowtie2 summary looks so weird that most read pairs are aligned neither concordantly nor discordantly: output:

4385453 reads; of these:

4385453 (100.00%) were paired; of these:

4354960 (99.30%) aligned concordantly 0 times
8872 (0.20%) aligned concordantly exactly 1 time
21621 (0.49%) aligned concordantly >1 times
----
4354960 pairs aligned concordantly 0 times; of these:
  8258 (0.19%) aligned discordantly 1 time
----
4346702 pairs aligned 0 times concordantly or discordantly; of these:
  8693404 mates make up the pairs; of these:
    1848948 (21.27%) aligned 0 times
    192386 (2.21%) aligned exactly 1 time
    6652070 (76.52%) aligned >1 times
78.92% overall alignment rate

Btw the command line was given by my instructor. I think he used option -X 3000. I don't know if the large insert size has an impact here. If so it should allow more concordant alignments right?

Command line: bowtie2 -1 159C_Unmapped.out.mate1 -2 159C_Unmapped.out.mate2 -S unmapped/Pacnes.sam --no-unal --no-head --no-sq -p 11 -X 3000 --local -x /dell/refs/bowtie2/Propionibacteriums-PA2

This is dual-seq containing both from human and bacteria. Bowtie2 is used here to map those unaligned by star using human genome onto bacteria genomes.

[James Ashmore]

It would help if you posted the command and also maybe told us what type of library you're aligning.

[zhangzhenyusz]

Hi. Thank you for the reply. I updated the post with command line and library using here.

[James Ashmore]

Run FastQC on your sequences, is it possible the majority of them are contaminate adapters?

[h.mon]

Dual RNAseq? Dual DNAseq? What kind of library preparation? Maybe the neither concordant nor discordant reads are from other bacteria?

Neither concordant nor discordant means unmapped, by the way.