CHIP-Seq data mapping using Bowtie2
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
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6466351 pairs aligned concordantly 0 times; of these:
742413 (11.48%) aligned discordantly 1 time
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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
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Ram
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tikshyadav19 •
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tikshyadav19 •
1 answer
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.
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