sequence-formatted file (.seq)

[zisis86]

How to obtain sequence-formatted file (.seq) from fas/fastq ?
I need the Arabidopsis Chromosome in seq format in order to use it in a pipeline for experiments

[maubp]

Do you have any example files to look at, or more information about what this sequence-formatted file (.seq) means?

I would guess they just mean a FASTA file using the extension *.seq instead of *.fasta, *.fas, etc.

[zisis86]

The example files that i have are in seq format and i cant open them!for example chr1.seq chr2.seq etc
I guess the same . Do you know any editor for Linux to convert Fastq in seq?

[westerman]

I think that the point Peter was making is: "What are .seq files?" These are not a common standard file. In order for us to help you, please give us an example of what you want and/or the name of the program of that wants these .seq files.

[GenoMax]

.seq files should just be fasta formatted sequence files.

If distant memory serves me right then they used to be produced from ABI sequence files when an external basecaller was used.

zisis86: Can you tell us what it is that you are exactly trying to do?

Note (looked this up): When ABI SCF files were processed with Phread, a .seq and a corresponding .qual files were produced.

[swbarnes2]

Sanger sequencing cores often return a .seq and an .ab1 file. So the .seq is just a plain text version of the sequence.

I don't think there are any rules about what a .seq has to look like, but they are almost certainly just text files, and you could open them in anything that can read text.

[zisis86]

Well i am trying to use this toolhttp://compgenomics.weizmann.ac.il/tanay/?page_id=367\ . It's a tool for analyzing 4C-seq experiments, including sequence extraction, mapping, normalization. I tried the example that this tool provides and i did it but it is complicated when you want to use another data set . For example i want to use data from Arabidopsis chromosome. In order to be able to run the experiments and the steps of this tool you need to have yous files at first at seq format. Also you have to convert fastq files in raw files etc. If you check this link there is a manual of the tool.

thank you

[sklages]

Having a look at the manual, ..

[...] the pipeline uses .seq files (note: these are distinct from fasta files) [...]

The chromosome seq files are just the plain sequence itself on one line, no header, no newlines.

Conversion of fastq data is documented.

[zisis86]

Thanks for the help.I think the same.
Is it possible to create a script in perl or other language to do this job? to read the lines from the fastq file and to write in another file on one line. Any ideas?

[westerman]

Lots of possible code ranging from complex and error-proof to simple and prone to error. Probably tons of pre-written programs as well. But since you asked, here is a nice cryptic perl script

perl -pe 'BEGIN{<>}; print $_; <>;<>;<>;' < input_file > output_file

[sklages]

Thanks for the help.I think the same.
Is it possible to create a script in perl or other language to do this job? to read the lines from the fastq file and to write in another file on one line. Any ideas?

Your reference data is fastq-formatted? If you talk about the read data, then you need to convert to "raw" format, described in "3.2 Converting fastq files to “raw” format".

And, .. just to add another one ;-)

perl -lne 'print if(($.+2)%4==0)' input_file > output_file