I sequenced a DNA-library obtained from soil samples using MiSeq system of Illumina. To account for contamination in the lab, I added a negative control. Unfortunately, this control was not added on the sample list, and hence, the sequences ended up in the Undetermined file.
Is there any way I can retrieve these sequences (they also have a specific barcode) from the Undetermined file using command lines?
Depending on the file type of the 'undetermined file', it can be easily performed in the command line. Assuming it's a Fastq file, you can use the barcode (You know the barcodes of interest, rigth?) as a query with the 'grep' command. You will have to fine tune the command with the 'after' option, in order to print or store the subsequent lines containing your sequences!
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