Question: Will not clip a fasta format file
0
gravatar for nalyo005
3.8 years ago by
nalyo0050
Canada
nalyo0050 wrote:

Hello,

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,

A.

galaxy • 755 views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by nalyo0050
0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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:

http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

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:
http://wiki.galaxyproject.org/Learn/CustomGenomes

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k
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