About fake reads

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Revision as of 08:19, 9 July 2010 (view source) Csbl (Talk | contribs) (Created page with '3.40) FAKE READS By "fake reads" I mean reads such as those created from a Genbank reference sequence or a consensus from some other assembly... or others for which there is no…') ← Older edit		Latest revision as of 08:38, 17 July 2010 (view source) Csbl (Talk | contribs)
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		+	'''fake reads 만들기'''
		+	1. panflam:/home/gnusnah/p-code/PModule/assembler_modules/make_fake_reads.py
		+	2. MIRA 의 scripts : fasta2frag.tcl -> single fasta에 대해서 사용가능 -> biopython으로 여러 fasta에 대해 사용 가능하도록 하는 스크립트 작성
		+
		+	http://standardsingenomics.org/index.php/sigen/article/view/sigs.952166/237
		+	위 논문에서 fake reads
		+	from 454 : consed 옵션으로 나온 폴더에 포함 (.ace 파일, phd파일)
		+	from velvet : contigs를 쪼개야함
		+
		+
	3.40)  FAKE READS		3.40)  FAKE READS
	By "fake reads" I mean reads such as those created from a Genbank		By "fake reads" I mean reads such as those created from a Genbank
		+
	reference sequence or a consensus from some other assembly... or others		reference sequence or a consensus from some other assembly... or others
		+
	for which there is no chromatogram (and there never was any		for which there is no chromatogram (and there never was any
		+
	chromatogram).  If you don't use any such reads, you can skip this		chromatogram).  If you don't use any such reads, you can skip this
		+
	step.		step.
	In the past, any read that ended with a .a2 or .c3 (where 2 and 3		In the past, any read that ended with a .a2 or .c3 (where 2 and 3
		+
	could be any numbers), was considered a fake read.  Now you can make		could be any numbers), was considered a fake read.  Now you can make
		+
	Autofinish not assume this using the .consedrc parameter (see CONSED		Autofinish not assume this using the .consedrc parameter (see CONSED
		+
	CUSTOMIZATION):		CUSTOMIZATION):
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	Instead, you must have determineReadTypes.perl put "fake" into the		Instead, you must have determineReadTypes.perl put "fake" into the
		+
	"type:" field of a "template" WR item.  See determineReadTypes.perl for		"type:" field of a "template" WR item.  See determineReadTypes.perl for
		+
	more information.		more information.

---

Latest revision as of 08:38, 17 July 2010

fake reads 만들기
1. panflam:/home/gnusnah/p-code/PModule/assembler_modules/make_fake_reads.py 
2. MIRA 의 scripts : fasta2frag.tcl -> single fasta에 대해서 사용가능 -> biopython으로 여러 fasta에 대해 사용 가능하도록 하는 스크립트 작성

http://standardsingenomics.org/index.php/sigen/article/view/sigs.952166/237

위 논문에서 fake reads
from 454 : consed 옵션으로 나온 폴더에 포함 (.ace 파일, phd파일)
from velvet : contigs를 쪼개야함

3.40) FAKE READS

By "fake reads" I mean reads such as those created from a Genbank

reference sequence or a consensus from some other assembly... or others

for which there is no chromatogram (and there never was any

chromatogram). If you don't use any such reads, you can skip this

step.

In the past, any read that ended with a .a2 or .c3 (where 2 and 3

could be any numbers), was considered a fake read. Now you can make

Autofinish not assume this using the .consedrc parameter (see CONSED

CUSTOMIZATION):

consed.fakeReadsSpecifiedByFilenameExtension: false

Instead, you must have determineReadTypes.perl put "fake" into the

"type:" field of a "template" WR item. See determineReadTypes.perl for

more information.