Raw reads from Ion Torrent. Is it single-end reads or paired-end reads.

Question

[eudaims]

Hi guys,

I got a raw data generated from Ion Torrent (Ion PGM) for sequencing virus species. The raw data in FastaQ format . Format of FastaQ tells you information about the reads. Normally, the first line tells you type of the reads (Is it single-end reads or paired-end reads).

My raw data has no information if the reads single-end reads or paired-end reads. I tried to contact owner of the raw data but I failed. My question is how do I know types of the reads?. Is there any tool can help me to know is the reads single-end reads or paired-end reads?. Is there something wrong during the sequencing?.

Thanks in advance for your help.

Basim

[eudaims]

Thanks anicet.ebou for your helpful reply.

Actually, the filename format like FILENAME_XXX.fastq.

Do you think it's single-end reads?

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[anicet.ebou]

Yes, if the filename format is like FILENAME_XXX.fastq then I'm almost sure that it is a single-end reads file.

[eudaims]

Your reply is very appreciated. Thanks again for your answer

[Kevin Blighe]

You should also be able to check the run parameters, no? ...or is this data that has just been lying around? You can also usually know via the headers within the file(s) itself.

Answer 1

[anicet.ebou]

Generally, if the reads are paired-end data, the filename should be something like FILENAME_XXX_R1.fastq and FILENAME_XXX_R2.fastq and otherwise, for single-end, it should be something like FILENAME_XXX.fastq. Do the name of your file is formated in such a way?