Question: Will not clip a fasta format file
gravatar for nalyo005
4.0 years ago by
nalyo0050 wrote:


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.

Thank you,


galaxy • 794 views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by nalyo0050
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


You will want to be working with either "fasta" format (assigned as the datatype) or with a "fastq" version that has been modified or confirmed to be in "fastqsanger" format (also assigned). 

Help with determining the type, and for checking/converting/assigning datatype - including any quality scores (even though it sounds as if you do not have these), please see the links here:

And even though you are not working with a Custom Reference Genome, the format is also fasta, and the guidance and format troubleshooting advice may help:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour