We used high throughput screening of small DNA fragments (about 100 base pairs long). The files are very large- i have filtered them on both the forward and reverse primer to screen out fragments of interest. However, when i try to clip these files it tells me that the file format is not fasta. Which is impossible because the file format is fasta, and also becuase i was able to filter them as such.
I cannot clip, sort or even collapse these files because the software will not recognize them as fasta format.
I have tried converting them to fasta and fastaq- but that has not worked.
I have downloaded the files and then uploaded them seperately but that has not worked either.
Please advise, any help would be appreciated.