Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • SRA to fastq

    Hi,

    I'm trying to convert an sra file to fastq. i downloaded the sra toolkit and ran fastq-dump, here's what i got:


    "Unrecognized character \xCF; marked by <-- HERE after <-- HERE near column 1 at fastq-dump line 1."

    can somebody help me, are there any other script to convert sra files to fastq?

    thanks,
    christine

  • #2
    Hi christine,
    can you provide the command you used and where you got the SRA file from. I don't think that fastq-dump is the problem, but rather your SRA file.

    Comment


    • #3
      Hi

      thanks for your reply. I ran this command, within the bin directory, - perl fastq-dump.2.3.5.2 SRR504687.sra. I also copied the sra file to the bin.

      I downloaded this rsa file from here http://www.ncbi.nlm.nih.gov/sra/SRX151862%5Baccn%5D

      thanks,
      Christine

      Comment


      • #4
        Originally posted by tinguzman View Post
        perl fastq-dump.2.3.5.2 SRR504687.sra.
        That's the problem. What you have is a pre-compiled binary, not a perl script. Simply running
        Code:
        ./fastq-dump.2.3.5.2 ./SRR504687.sra
        from within your bin directory should work.

        Comment


        • #5
          Hi,

          thanks a lot! it's working now.

          best,
          christine

          Comment


          • #6
            hi again!

            i just finished running ./fastq-dump.2.3.5.2 -split-files ./SRR504687.sra. i have 2 output SRR504687_1 and SRR504687_2. one is 13gb while the other is only 3gb. i'm expecting that they should have the same size, for forward and reverse reads, right? correct me if i'm wrong coz i'm planning to assemble them using trinity. should I qc them first?

            best,
            christine

            Comment


            • #7
              You can download the compressed fastq files from ENA (here and here). That's often faster than dealing with SRA, since the SRA toolkit is painfully slow and often buggy. You'll note that their fastq files also have a different size, so this isn't something you're doing wrong.

              Comment


              • #8
                Hi Ryan,

                thank you very much. submitted fastq files or sra files are not yet trimmed/filtered right? they are raw sequences, for example from illumina sequencing.

                best,
                christine

                Comment


                • #9
                  Yeah, they should be the raw files. This definitely raises the question of why the files have such different sizes. My guess is that the only person that can really answer that is the person that uploaded the files (Ana Riesgo).

                  Comment


                  • #10
                    Originally posted by tinguzman View Post
                    hi again!

                    i just finished running ./fastq-dump.2.3.5.2 -split-files ./SRR504687.sra. i have 2 output SRR504687_1 and SRR504687_2. one is 13gb while the other is only 3gb. i'm expecting that they should have the same size, for forward and reverse reads, right? correct me if i'm wrong coz i'm planning to assemble them using trinity. should I qc them first?

                    best,
                    christine
                    I should have mentioned that the -split-3 command is always preferred over "split-files". This way 1 file will be generated for single end data, 2 files (with sufffix "_1" and "_2") for paired ends and 3 files (suffix "_1", "_2" and w/o suffix) if there are reads without mate pairs. This way I get a 13.2Gb file ("_1") and a 7.0Gb file ("_2") from the sra.
                    Looking at the fastq files, you'll see that forward reads are 150bp while reverse are 48bp. I have actually never seen this for PE data before and would contact the uploader (as dpryan suggested). At least there are no missing mates... I would give it a try and use them in trinity while waiting for an answer.

                    Comment


                    • #11
                      Has anyone had any issues downloading and splitting files from dnanexus? I'm unable to use aspera connect to download files from sra. I'm trying to replicate an experiment to test out an RNA-seq analysis pipeline but am having issues with 3 particular files. SRR639124, SRR639239, SRR639263.

                      The sra toolkit is working as other files has split without issue. SRR639124 oddly splits to two files _1 is 100bp and _2 is only 1bp? The other two will not split. The stat script shows only 1 read.

                      I'm wondering if it's an issue with dnanexus or the original SRA upload. Any help would be appreciated.

                      Comment


                      • #12
                        Are you using the latest sratoolkit? You no longer need to download .sra files. fastq-dump from the new sratoolkit will download fastq files directly.

                        Comment


                        • #13
                          Originally posted by GenoMax View Post
                          Are you using the latest sratoolkit? You no longer need to download .sra files. fastq-dump from the new sratoolkit will download fastq files directly.
                          I believe so. Using 2.4.3.

                          How exactly does that work? curl?

                          Comment


                          • #14
                            Originally posted by lac302 View Post
                            I believe so. Using 2.4.3.

                            How exactly does that work? curl?
                            See this: http://seqanswers.com/forums/showpos...36&postcount=7

                            BTW: SRR639124 appears to be a single end dataset irrespective of what the SRA record says (this type of thing happens at times).

                            Comment


                            • #15
                              Thanks Geno. I need to improve my search skills.

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Strategies for Sequencing Challenging Samples
                                by seqadmin


                                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                                03-22-2024, 06:39 AM
                              • seqadmin
                                Techniques and Challenges in Conservation Genomics
                                by seqadmin



                                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                Avian Conservation
                                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                03-08-2024, 10:41 AM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, Yesterday, 06:37 PM
                              0 responses
                              10 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, Yesterday, 06:07 PM
                              0 responses
                              9 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-22-2024, 10:03 AM
                              0 responses
                              50 views
                              0 likes
                              Last Post seqadmin  
                              Started by seqadmin, 03-21-2024, 07:32 AM
                              0 responses
                              67 views
                              0 likes
                              Last Post seqadmin  
                              Working...
                              X