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Hi all!
Is any mapping tools designed for 454 cDNA data?
BWA seems not work well with 454 data.
Hope for some suggestion.
Is any mapping tools designed for 454 cDNA data?
BWA seems not work well with 454 data.
Hope for some suggestion.
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If you can get access to the Roche tools, gsMapper might be a tool to try. -
Thanks you. I have account for gsMapper. But it seems that gsMapper doesn't account for junction reads but I hope those included.Originally posted by flxlex View PostComment
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What do you mean by junction reads? Do you mean mapping transcriptome reads in an intron/exon aware way?Comment
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Yes.take splicing into account. some reads may be mapped to the junction of two exons separated by an intron on the chromosome.Originally posted by maubp View PostComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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