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Hi
I am mapping paired-end reads on genome (E. coli and Trypanosoma) using Bowtie2. RNA sequenced was 18-300 nt.
Parameters are following --rdg 50,3 --rfg 50,3 -a --phred64 -N 1 --no-mixed
The problem I encounter is that many short reads that originate from RNA-s which have posttrancriptionally added bases at 3' end are not mapped. In case on Trypanosome CCA is added to the 3', in case of E. coli poly-A can be added.
I noticed if read length is upto 24 bases and it cointains CCA in the 3'end, then the reads are not mapped. If only CC is at the 3' end, then reads upto 22 bases are not mapped.
Can anybody recommend how to proceed or what parameters of Bowtie2 should I use to so that short reads with 3' mismatches would be mapped also?.
I option I could think of is to use local alignment mode but then I am afraid that I might get more mapping for other reads and it makes difficult to go further. Or would be even a better idea to run unmapped reads with local mode?
I am mapping paired-end reads on genome (E. coli and Trypanosoma) using Bowtie2. RNA sequenced was 18-300 nt.
Parameters are following --rdg 50,3 --rfg 50,3 -a --phred64 -N 1 --no-mixed
The problem I encounter is that many short reads that originate from RNA-s which have posttrancriptionally added bases at 3' end are not mapped. In case on Trypanosome CCA is added to the 3', in case of E. coli poly-A can be added.
I noticed if read length is upto 24 bases and it cointains CCA in the 3'end, then the reads are not mapped. If only CC is at the 3' end, then reads upto 22 bases are not mapped.
Can anybody recommend how to proceed or what parameters of Bowtie2 should I use to so that short reads with 3' mismatches would be mapped also?.
I option I could think of is to use local alignment mode but then I am afraid that I might get more mapping for other reads and it makes difficult to go further. Or would be even a better idea to run unmapped reads with local mode?
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