Question: troubleshooting bowtie2 low mapping rates
0
gravatar for F
3.1 years ago by
F3.4k
Iran
F3.4k wrote:

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

myposts rna-seq • 1.6k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by F3.4k

Firstly why are you mapping to the transcriptome?

ADD REPLYlink written 3.1 years ago by mark.ziemann1.1k

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 didnt try if the input file are allowed for my script 

ADD REPLYlink written 3.1 years ago by F3.4k

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

ADD REPLYlink written 3.1 years ago by mark.ziemann1.1k

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

ADD REPLYlink written 3.1 years ago by F3.4k
1

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)

ADD REPLYlink written 3.1 years ago by mark.ziemann1.1k

thank you for your comment

ADD REPLYlink written 3.1 years ago by F3.4k
2
gravatar for F
3.1 years ago by
F3.4k
Iran
F3.4k wrote:

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

ADD COMMENTlink written 3.1 years ago by F3.4k
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