Entering edit mode
8.6 years ago
zizigolu
★
4.3k
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
Firstly why are you mapping to the transcriptome?
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 scriptRibo-seq. Good to know. Did you clip the adapter sequences?
I trimmed the adapter by universal illumina adapter sequence but the rate of trimmed reads was zero.
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)
thank you for your comment