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Old 09-27-2010, 11:24 PM   #1
Kevin_YY
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Default Need reverse reads or not?

Dear All,

When we assemble sequences by using program such as MIRA or Velvet, do we need to make sure that all the reverse reads were turned into the forward one? Or just put all the forward and reverse reads in one fasta file.

Thx
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Old 09-28-2010, 01:49 AM   #2
maubp
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What kind of paired end data are you starting with?

For velvet, you need one file for paired reads where they are interleaved (forward read then reverse read), and a separate file for any single reads.

For MIRA, you put all the paired reads in the same input file (either a FASTA + matching QUAL file, or a FASTQ file). The reads must be named so as to identify the pairs, and yes, the reverse reads should be inwards as though done with Sanger end sequencing.

Basically read the MIRA or Velvet documentation
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Old 10-02-2010, 06:57 PM   #3
Torst
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Quote:
Originally Posted by maubp View Post
For velvet, you need one file for paired reads where they are interleaved (forward read then reverse read), and a separate file for any single reads.
Actually Velvet does not care what direction they face, as long as they are opposite... for example, if you feed it (<= =>) mate pairs, it can estimate (or you can supply) an insert size of -3000 bp (negative 3000) ... but I wouldn't trust the code completely!

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Originally Posted by maubp View Post
Basically read the MIRA or Velvet documentation
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Old 10-03-2010, 12:12 AM   #4
anyone1985
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you mean velvet can reverse the reads itself, even if it is mate pairs. however, in the mailing list, more than one time, they have mentioned to reverse both of the two reads to assemble the mate pairs

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Originally Posted by Torst View Post
Actually Velvet does not care what direction they face, as long as they are opposite... for example, if you feed it (<= =>) mate pairs, it can estimate (or you can supply) an insert size of -3000 bp (negative 3000) ... but I wouldn't trust the code completely!



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