troubleshooting bowtie2 low mapping rates

Question

[zizigolu]

Hi,

I am mapping my illumina reads on the transcriptom by bowtie2 but the rate of alignment is too LOW(0.9). When I tried my reads on genome the alignment increased 3 times. anyway I have to use transcriptome by bowtie2 (I should not use tophat), then with which option I can truncate my reads to 50 bases?

I tried this option but

bowtie2 -x CDS -N 2 -L 28 -X 50 -U SRR1688549-ribo.fastq -S SRR1688549.sam

Thank you for your help

[mark.ziemann]

Firstly why are you mapping to the transcriptome?

[zizigolu]

we are working on ribosome drop-off then the R script we are using to calculating the slop needs three input file, bed file from ribo-seq, and two txt files from ribo-seq and rna-seq contains the number of reads mapped on each gene. Anyway I tried tophat but no way to get such an input there then I should used bowtie2 but because I am working with yeast I should consider interons then I should use transcriptome. Anyway the mapping rate is too vary and sometimes too low. then I used --local option in bowtie2 even the mapping rate increased three times I didn't try if the input file are allowed for my script

[mark.ziemann]

Ribo-seq. Good to know. Did you clip the adapter sequences?

[zizigolu]

I trimmed the adapter by universal illumina adapter sequence but the rate of trimmed reads was zero.

[mark.ziemann]

Is your library tagged with universal illumina or something else? Small RNA, CAGE and Ribo sequencing protocols often use custom adapters. You can diagnose adapter sequences with Minion (Kraken suite)

[zizigolu]

thank you for your comment

Answer 1

[zizigolu]

use --local option then the rate of mapping will increased 3 times!!!