[khmer] Issue interleaving reads with cutadapt processed fastq

[Fields, Christopher J]

I may be mis-remembering this, but I recall cutadapt giving empty sequences with paired data before (maybe this has been fixed).  Are any of the sequences empty?

chris

On Sep 16, 2015, at 12:27 PM, Will Shoemaker <wrshoema at umail.iu.edu<mailto:wrshoema at umail.iu.edu>> wrote:

Hello,

I am unable to merge pairs of MiSeq reads using the khmer scrip interleave-reads.py in khmer version 1.3. The R1 and R2 files have had the first 10 bases trimmed off and have been quality filtered using cutadapt v1.9.

Using the command zcat file_name.fastq.gz | echo $((`wc -l`/4)) on each set of reads, I found that the number of reads in R1 and R2 is the same.

The command I'm running is:
interleave-reads.py -o output.fastq.gz R1.fastq.gz R2.fastq.gz   (file names changed for readability)

My OS is Linux 2.6.32-573.3.1.el6.x86_64 x86_64

Attached is a txt file of the khmer output.

Could this be an issue of cutadapt changing the file format? I am able to run assemblies on cutadapt processed reads.


Best,
Will Shoemaker
--
Will Shoemaker
Indiana University
Graduate Student: Lennon Lab
Evolution, Ecology, & Behavior Program
Jordan Hall 238
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