Hi,
I have bunch of formerly paired-end-reads that are now combined together (overlapping PE-reads) and the reads have unique names pointing to sample groups. (Frex. >uniqueid_groupA etc.). It is no problem to bin them to different fastq-s containging sequences from different samples. (Frex groupA.fastq, groupB.fastq).
The combining and binning was done externally form mothur and also the barcodes and primers removed - would it still be possible to use mothurs make.sra command to build an sra file out form those files.
it seems to be a simple case of feeding the data with an option to show which fastq files should be associated with which samples - like group A - groupA.fastq - unfortunatley such an option seems to be only present for paired and fastqs where you can add groupA GroupAR1.fastq and GroupAR2.fastq.
Would it by some trickery still be possible to use file= or other parameters to accomplish my goal with single-combined fastq files and group parameters.
If not I’d like to make it as a feature request for make.sra. If I know how my fastq files are associated with samples then I should be able to use these without inputing barcodes information. Especially if such an option already exists for pairs of fastq-s containing non-merged PE reads.
You are correct the make.sra command only accepts the paired file format currently. We can certainly add a modification to the command to allow for the format you are talking about. Perhaps something like:
groupA filename NONE
Thanks for the feature request!