Question: Raw reads from Ion Torrent. Is it single-end reads or paired-end reads.
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gravatar for eudaims
10 weeks ago by
eudaims0
eudaims0 wrote:

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

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by eudaims0

Thanks anicet.ebou for your helpful reply.

Actually, the filename format like FILENAME_XXX.fastq.

Do you think it's single-end reads?

ADD REPLYlink written 10 weeks ago by eudaims0
1

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.

ADD REPLYlink written 10 weeks ago by WouterDeCoster42k

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

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by anicet.ebou160

Your reply is very appreciated. Thanks again for your answer

ADD REPLYlink written 10 weeks ago by eudaims0

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.

ADD REPLYlink written 10 weeks ago by Kevin Blighe53k
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gravatar for anicet.ebou
10 weeks ago by
anicet.ebou160
anicet.ebou160 wrote:

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?

ADD COMMENTlink written 10 weeks ago by anicet.ebou160
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