CHIP-Seq data mapping using Bowtie2

Question

[tikshyadav19]

The sequence samples were trimmed and all adapters were removed but still while mapping Rice ChIP seq data I got mapping results as:

17934395 reads; of these:
  17934395 (100.00%) were paired; of these:
    6466351 (36.06%) aligned concordantly 0 times
    5965884 (33.27%) aligned concordantly exactly 1 time
    5502160 (30.68%) aligned concordantly >1 times
    ----
    6466351 pairs aligned concordantly 0 times; of these:
      742413 (11.48%) aligned discordantly 1 time
    ----
    5723938 pairs aligned 0 times concordantly or discordantly; of these:
      11447876 mates make up the pairs; of these:
        9455736 (82.60%) aligned 0 times
        412835 (3.61%) aligned exactly 1 time
        1579305 (13.80%) aligned >1 times
73.64% overall alignment rate

Cannot resolve the reason for the low map. The indexed genome is Rice genome as the CHIP data is of Rice. Need your kind suggestions.

Thank you

Tikshana

Answer 1

[Qiongyi]

Low mapping ratio may be due to contaminations or poor quality of your sequencing libraries. You can use fastq_screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) to check where your reads come from.