Hello
I download some data from EBI website. So these datas are small rna seq data and the types are Fastq.gz. Is there any way to converting them to fastqsanger, i mean some how remove the gun zip(gz). ? I try that with changing their data set manually but in mapping step it make some errors.
Thanks
Just unpack it…
For example with the command:
gunzip myfile.fastq.gz
This is not really a galaxy question and a very basic thing to do so it is possible I understand your question wrong.
EDIT:
If you are on windows I think you could use 7zip.
I am asking because i do not actually download the files. Im downloading it directly in to galaxy. So i have not any data to use gunzip or 7zip.
I was asking about Gunzip files in GALAXY. (to get results faster, otherwise i know if i download them, i can use gunzip on ubuntu
Then indeed I did not fully understood it, already had that feeling. Most mapping tools can handle .gz files. Maybe if you share which tool you used and the error people can better help you. Or maybe it helps if you download the files and check whats in it.
My data is fastq.gz . so the bowtie doesnt recogonize this type of dataset. So i wondered if maybe i can convert them with some tools in galaxy
@amir please tell Galaxy that this datatype is fastqsanger.gz I think then it will work.
i tried that. but makes some errors in mapping steps
What kind of errors? Can you share a history?
it says my data isnt fastq file. it happens when i do what you said
If still not clear i can share the history
Hi amir - I know this is a rather belated response but bowtie2 requires that it’s input files be in the .fastqsanger/.fastqsanger.gz format which is effectively the same as fastq but provides a guarantee that the PHRED quality encoding is the more recent version. You can designate your file as fastqsanger at upload, edit their format from the history or feed them through the fastq groomer tool to convert them to fastqsanger
Thanks it solved one of my biggest issues.