Tool:CHIP-Seq data mapping using Bowtie2
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3 months ago

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

ChIP-Seq Mapping Tool • 231 views
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Entering edit mode
3 months ago
Qiongyi ▴ 110

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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