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  • fastq-dump on SRA files

    Hello, I have a question about .sra files.
    I've downloaded the .sra files from this dataset.

    SRR039628.sra
    SRR039629.sra
    SRR039630.sra
    SRR039631.sra
    SRR039632.sra
    SRR039633.sra

    However, after running

    ./fastq-dump -A SRR039628 SRR039628.sra

    I only get 1 file: SRR039628.fastq. I thought on paired end reads I would get 3 files SRR039628_1.fastq and SRR039628_2.fastq along with SRR039628.fastq. Am I doing something wrong?

  • #2
    All of the mentioned runs are fragments - single read

    Comment


    • #3
      hi,

      I have downloaded a file from SRA and used fastq-dump..

      However when I check my output .fastq file I see this



      head -10 SRR036210.fastq
      @SRR036210.1 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_144 length=25
      T2030201230313112312001111
      +SRR036210.1 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_144 length=25
      !"""""""""""""""""""""""""
      @SRR036210.2 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_198 length=25
      T2030201230313112312001111
      +SRR036210.2 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_198 length=25
      !"""""""""""""""""""""""""
      @SRR036210.3 VAB_S0040_20080711_Legend_quad_2_NK_Act_462_9_1360 length=25
      T2030201230313112312001111


      Any suggestions?

      cheers,

      Nandan

      Comment


      • #4
        That's a colorspace fastq file. From the bit you posted it looks OK, but you'll need to use colorspace aware tools to do anything with it.

        Comment


        • #5
          fastq-dump defaults to colorspace for SOLiD technology.
          You can use '-B' option to force translation into basespace if you wish - the only downside - all bases after miscalled color '.' will become 'N'

          Comment


          • #6
            Originally posted by srasdk View Post
            All of the mentioned runs are fragments - single read
            Thank you for the reply.

            Comment


            • #7
              Thanks everyone

              Comment


              • #8
                I'm having the same basic problem as the original poster in this thread.
                I downloaded the file: SRR063783.sra, and ran fastq-dump on it.

                It's supposed to be paired-end data, but I'm only getting a single file: SRR063783.fastq

                In this file it looks as though each pair of forward and reverse reads has been combined into a single sequence. Is there a way to split them up again?

                Comment


                • #9
                  Try fastq-dump -SL

                  Comment


                  • #10
                    Originally posted by Benjamin Vincent View Post
                    Try fastq-dump -SL
                    This did the trick. Thank you very much.

                    Comment


                    • #11
                      To Convert SRA to Fastq

                      use this command

                      open SRA toolkit kit path

                      open bin folder

                      fastq-dump.exe pathfile\filename outputfilename

                      Comment


                      • #12
                        fastq-dump --split-files --gzip ./SRR1232309.sra

                        Comment


                        • #13
                          Hi,
                          Been using fasterq-dump.2 to download and save fastq files.
                          How can I download the fastq files using fasterq-dump and still keep original read names with details about each read as seen on ncbi website?

                          site: https://www.ncbi.nlm.nih.gov/sra

                          Comment


                          • #14
                            Converting SRA files into Fastq

                            Hi I am new to bioinformatics I did some courses online and loved it which doesn't mean I find it easy! On the contrary and I really admire you guys who can get around it!

                            First step, I want to get SRR7962225 as fastq format.

                            I downloaded the data sra_data.fastq.gz and the SRA toolkit but it refuses to convert it using fastq-dump however I get something like

                            2·43222Õ3Ô3T0TÈIÍK/É°540ä ÿÿ,ŒÁ......etc

                            using Notepad.

                            Any suggestions?

                            Comment


                            • #15
                              Some more details about the commands you have run would be helpful. If the file has a .gz extension then it needs to be unzipped first. I may be wrong but it sounds like you are on a windows os so try 7zip to decompress. Depending on your objective you might be limited on the analyses you can perform on windows os.

                              Comment

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