Bowtie mapping for single_end read

Question

[Rita]

bowtie --threads 5 -X 1000 -m 1 -v 2 --best --strata --sam IndexedGenome ${DATA_DIR}${SRR_ID}.trim.fastq > ${SAM_DIR}${SRR_ID}.sam

Hi All,

I am using the above script to map single_end ChIP-Seq reads. The percentage of the aligned reads is around 20%. How can I modify the script to achieve a better alignment rate?

[Tao]

Maybe you could use bowtie2 instead of bowtie

[Rita]

Thank you, Tao. We prefer bowtie to bowtie2 in this case.

[ATpoint]

I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChIP-seq the most likely explanation is that the sample is mostly of poor quality. Make a bigwig file out of the mapped reads and inspect on a browser if you see any evidence for peaks. Make also sure that reference genome is correct.

[Rita]

Thank you, ATpoint!