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Hi All:
I am new to NGS work. I am currently working on de novo assembly of transcriptome. While working with 454 data I noticed that there are some bases in the filtered/trimmed read with areas where quality is less than the threshold used for trimming/filtering. Is is a common thing. If so how it can be worked out or justified during assembly. I am using some perlscripts for quality trimming. In assembly these bases are masked ( ie in lowercase letters).
Another question, in the 454Read Status file many of the reads are designated as singletons. Are these reads included in the AllContig file or isotig file?
Thanks in advance and I appreciate your help.
Can any one direct me to any of the literature that explains all these thing about assembly.
I am new to NGS work. I am currently working on de novo assembly of transcriptome. While working with 454 data I noticed that there are some bases in the filtered/trimmed read with areas where quality is less than the threshold used for trimming/filtering. Is is a common thing. If so how it can be worked out or justified during assembly. I am using some perlscripts for quality trimming. In assembly these bases are masked ( ie in lowercase letters).
Another question, in the 454Read Status file many of the reads are designated as singletons. Are these reads included in the AllContig file or isotig file?
Thanks in advance and I appreciate your help.
Can any one direct me to any of the literature that explains all these thing about assembly.