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Old 02-12-2014, 07:48 AM   #1
rozitaa
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Location: Sweden

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Default how will manipulating low quality base pairs of reads affect TopHat and Cufflinks?

Hi all,

I am working with a paired-end Illumina 2*250bp reads (16S rRNA). The quality is extremely low (i.e. with quality filtering only 24% of my reads remain with having all base pairs quality more than 20). As usual I have falling quality at the ends. The good thing about this data is: the pairs have about 240bp overlap. I would like to use this in order to increase the quality at the ends. I want to align ends and for each base pair that I get match between Fw and Re reads, put quality 40. Now the question will raise that: if I manipulate quality like that, the aligning part (with TopHat) and reading counts (with cufflink or htseq-count) will be affected because of having artificial high quality some parts and natural lower quality at other bases or not?

Thanks!
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