Bowtie --Col-Keepends Option

Question

[bioinforupesh2009.au]

Hello to all NGS experts,

Just a quick question from your experience.

I would like to align my small RNA reads of SOLiD color space data with bowtie. Therefore, its worth to define --col-keepends (to keep first and last color after alignment) flag that bowtie suppose not to have as default. ???

In my point of view bowtie dealing with, in the right way !!!!

May i should have this option --col-keepends or not ??? what is the benefit or disadvantage if i don't have this option ??

Help me plsss ??? to short-out my doubt ???

Answer 1

[Ashutosh Pandey]

The advantage of using color space read is that each nucleotide in the read is read twice (except at the start and the end) and this information is coded and shared between two positions located next to each other in the colorspace read (Read this: Transforming and manipulating color space reads). So, the aligner is pretty confident about the calls for all the nucleotides except the ones in the beginning and in the end. So, after alignment when bowtie decodes the colorspace alignment it trims off the first and the last color base from the read because it is not that confident about their decoding. I think it is a good practice when using bowtie to not to use "--col-keepends" as it may reduce false-positives calling of SNPs.

[bioinforupesh2009.au]

hello ashutoshmits,

Really thanks for your time and explanation it will be really help me out. Even i was thinking the same that bowtie is dealing the same by default as per your view but i have still a doubt. As i am working on small RNA-seq (miRNA) and one of my colleague is working on RNA-seq (mRNAs), However, he is using tophat for his analysis. As you know Tophat using bowite as for alignment and by default he has set the option "--col-keepends" that means suppose to keep first and last color after alignment. WHY ??? if your assumption is true about not to get FALSE SNPs.

Thank you once again and looking forward to get your more view as per your experiences.