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Old 02-12-2014, 08:48 AM   #1
Location: Sweden

Join Date: Jun 2013
Posts: 51
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?

rozitaa is offline   Reply With Quote

16s rrna, cufflink, quality filtering, tophat

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