read identifier causing error in make.contigs??

Commands in mothur
#1

Hi all,

I am very new to mothur and am attempting to process a hiseq dataset through the mothur MiseqSOP.

In the make.contigs command I am given the following warning repeatedly, seemingly for all reads in each groups fastq files.
[WARNING]: did not find paired read for HISEQ_224_H08R9ADXX_1_1106_16407_64100_1_N_0_TCGAAG, ignoring.

I am providing an R1 and R2 fastq file for each group of sequences, and a stability.files with the group name, R1 filename, R2 filename properly formatted.

I wonder whether the error is to do with the hiseq read identifiers, which look like this (see below) after being outputted from the program geneious in which I have trimmed off barcodes and primers…

@HISEQ:224:H08R9ADXX:1:1101:4423:2179_1:N:0:TCGAAG

Could it be that the ‘_’ prior to the read number as compared to a ‘space’ prior to the read number in typical Miseq read identifiers is causing the problem?

Many thanks in advance,

Chris.

#2

Answered my own question by editing the read identifiers using ShortRead package of bioconductor for R.

The underscore had to be replaced with a blank space and then make.contigs worked fine.

Chris.