Moderator: genomax
genomax ♦ 33k
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Posts by genomax
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... If there is independent experimental validation across many samples then it may be acceptable but you would still have to explain why contamination exists at that high level.
That said, consider this quote from ContEst paper
> a typical cancer project might expect >10% of the samples to ha ...
written 1 hour ago by
genomax ♦ 33k
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... I don't think we can answer this question without full context as @andrew said above. In general, if something was contaminated then your conclusions are always going to have a cloud hanging over them (unless there is a clear experimental case/explanation for presence of that contamination). ...
written 1 hour ago by
genomax ♦ 33k
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... What do *you* think? If you were reviewing such a paper would you consider this acceptable? How did the contamination occur in first place? ...
written 1 hour ago by
genomax ♦ 33k
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... Tumor is contaminated with what? ...
written 2 hours ago by
genomax ♦ 33k
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... It helps to specify if you are looking for a free resource or are willing to pay (something). If latter then Biostar handbook is linked by @st.ph.n. If former then take a look at [WikiBooks entry here][1].
[1]: https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS) ...
written 2 hours ago by
genomax ♦ 33k
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... You don't need to install since it is a stand alone executable. All you should need to do is make the file executable by doing `chmod u+x faSomeRecords` and then run it `./faSomeRecords orf_coding_all.fasta file_w_id extracted.fa` ...
written 3 hours ago by
genomax ♦ 33k
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... I gave you the example command line above. ...
written 4 hours ago by
genomax ♦ 33k
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... See this [thread on SA][1] and my answer there.
[1]: http://seqanswers.com/forums/showthread.php?t=75116 ...
written 4 hours ago by
genomax ♦ 33k
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... Get the sequence of all ORF's from [here][1]. Then use [faSomeRecords][2] from Kent Utilities from UCSC (with your ID's of interest in a file, one ID per line) to extract those 600 fasta files. `faSomeRecords orf_coding_all.fasta file_w_id extracted.fa`
[1]: https://downloads.yeastgenome.org/seq ...
written 4 hours ago by
genomax ♦ 33k
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... What do you mean you can't download sequence from SGD (e.g. [YAL063C][1] which is also called FLO9).
[1]: https://www.yeastgenome.org/locus/S000000059/sequence ...
written 4 hours ago by
genomax ♦ 33k
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