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[QUOTE=AJERYC;88920]Originally posted by gensdei View PostCell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?
Theoretically a cell line is homozygous and that is more easy to resolve with NGS so you could go 10-30x.Last edited by gensdei; 11-10-2012, 11:31 PM.
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[QUOTE=gensdei;88907]Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?
Theoretically a cell line is homozygous and that is more easy to resolve with NGS so you could go 10-30x.
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Cell lines have the benefit of being a relatively pure population of clonal cells and thus represent a particular snapshot of cancers. Is there anybody who have seen a paper using exome-seq with 100x coverage based on cell line? If there is not, does it means that we don't need perform that deep sequencing due to its purity?
Thanks in advance!
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Originally posted by AJERYC View Post30x is definitely not enough, since it means 30x averge, so you will get a lot of regions with very few sequences, that will make impossible for you to resolve heterozygous mutations. Go 50x or 100x.
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30x is definitely not enough, since it means 30x averge, so you will get a lot of regions with very few sequences, that will make impossible for you to resolve heterozygous mutations. Go 50x or 100x.
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exome sequencing
hello every body, i'm a new member and hope that you help me
i want to perform an exome sequencing on oral cancer cases using illumina. i need you to help me with a good protocol for doing so
thanks
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hello every body, i'm a new member and hope that you help me
i want to perform an exome sequencing on oral cancer cases using illumina. i need you to help me with a good protocol for doing so
thanks
Leave a comment:
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Exome sequencing
Hey I am trying to sequence the melanoma exome to find somatic mutation involved in the melanoma. I am very new to this technique and I have some questions regarding this:
1)Generally how many exomes from different melanoma samples need to be done to get some satisfactory results?
2)What coverage is essential for such a study? Initially I was thinking of around 30X but some papers have used nearly 100X. Will I be okay with 30X coverage of the exome?
Your help is well appreciated.Tags: None
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