[mira_talk] Paired end + single solexa input files

  • From: Matthew Baranski <matthew.baranski@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 13 Nov 2009 09:05:18 +0100

Hi all,

 

I am a bit unsure about how to structure my input Illumina fastq files. I have:

 

Paired end Illumina fastq file + 'single end' Illumina fastq file

 

However, the single end file actually consists of 'left-over' reads from the original paired end files (could have either /1 or /2 tags), where one of the mates has been removed as a result of pre-processing

 

Specifically:

 

Can I input paired-end data where some of the pairs are missing their mates? How will those single reads be treated?

Is there any other way I should input both paired end and single end reads together?

 

Thanks,

Matt 


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