User: Bach
Bach • 540
- Reputation:
- 540
- Status:
- New User
- Location:
- Website:
- http://www.chevreux.org/
- Last seen:
- 5 years, 2 months ago
- Joined:
- 8 years, 3 months ago
- Email:
- b***@chevreux.org
Author of the MIRA sequence assembler
Posts by Bach
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... For trying overlap based assemblers: absolutely do reduce the data set. Maybe to something like ~80x, but not really much more. Say, 40x from your merged reads, 40x from still paired reads. Then try out any of the usual suspects.
My first try would be with MIRA, but that is just because I wrote it. ...
written 6.0 years ago by
Bach • 540
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... Yes, see my comment to Neil's answer.
...
written 6.1 years ago by
Bach • 540
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... Searching via TITLE is a too strong restriction as it misses entries like EGC38264.1 (Title: "hypothetical protein DICPUDRAFT_149064 [Dictyostelium purpureum]") which does not have polyketide in the title but a nicely annotated polyketide synthase in the FEATURES section.
I suppose I'll have to writ ...
written 6.1 years ago by
Bach • 540
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... Dear all,
I am trying to get from the NCBI all proteins which have something to do with polyketides. Easy enough it seems, simply enter the search term "polyketide" into the Entrez form for protein searches and one gets back a nice list which can be downloaded in different formats:
http://www.ncbi ...
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... MIRA will also give you strain sequences, use convert_project for that
...
written 6.6 years ago by
Bach • 540
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... The RSS feed for BioStars on StackExchange was in a mode where each question was re-injected into the feed when a new answer or a new comment was added. Which was extremely convenient at times when someone added a new point of view to some older posts.
Does this kind of feed also exist for BioStar? ...
written 6.7 years ago by
Bach • 540
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... No, it is not. Simple example: "AAAA" as genome. I do agree though that this example is a bit far fetched :-)
...
written 6.8 years ago by
Bach • 540
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... "not commonly seen" is a nice expression. I never saw it and would probably never think of doing it: all these technologies are more or less "short read" atm. Ion + Illumina could make sense by mixing Ion 200+bp reads with Illumina 100-150bp, one cancelling the artifacts of the other. I do not see t ...
written 6.8 years ago by
Bach • 540
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Answer:
A: Fastq With Format Errors
... After you made sure that the errors are in the original data downloaded from ENCODE, I think the most important step you have to take is to notify the ENCODE project about this problem. Be polite, show them the problematic areas like you did here and ask them whether they could fix it ("pretty pleas ...
written 6.9 years ago by
Bach • 540
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Comment:
C: Weird Lines Of Fastq File
... I'll second the "corrupt" statement. It's nothing which should ever come out as FASTQ. Look upstream for any program which might have scrambled your data. ...
written 7.2 years ago by
Bach • 540
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