Question: bowtie2 summary looks very weird. Neither concordant nor discordant.
gravatar for zhangzhenyusz
2.6 years ago by
zhangzhenyusz20 wrote:

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.

rna-seq bowtie2 • 1.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by zhangzhenyusz20

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

ADD REPLYlink written 2.6 years ago by James Ashmore2.8k

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

ADD REPLYlink written 2.6 years ago by zhangzhenyusz20

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

ADD REPLYlink written 2.6 years ago by James Ashmore2.8k

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.

ADD REPLYlink written 2.6 years ago by h.mon29k
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