Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to make SRA downloaded fastq (PacBio RS I reads) acceptable for Falcon

    I am new in Pac-Bio seq analysis and doing some initial test run in Falcon.

    I have a downloaded dataset (Pac-Bio RSI reads) from SRA, and converted it to *.fastq, it looks like this:

    @SRR1168519.1 length=302
    ATTTTTGTCTGTCCGATTCTGATAGCAGGC
    GCATATCAGATGAATCTGATGAGTCAACACTGGTTGGTTCGTTGCTCAGTAGTTATGTTCGTGTGGAGCGTCGTATTGGTATCGAGTCTGATTGTCAGTCATCGATGGTCATTAGTCACGTCCTTCCAGTAGTTCGTATCAACATGCTTCACTATTCTTGTTGTTGTAGATGTTATTCGTATTAGTGTGAGTGTCAGTAGTTACGCGTACAGTATCGGGATTTCGTAGCAGCGCGCGGCGTTGCGGAGTCAAGATTCATGGCTGGACTACGG
    +SRR1168519.1 length=302
    !"!!!"#$"##!!!"!!"!"#""""#$#"!"!""!!!!!""%"""!"!"#""!#"!!!"!#"!#!!!"!!!"""!!!!"""#!!"#"!"!""!"!!!!""#!!!""!!!"!#!"###"#""!"!!!##!#!#!"!"""!"$$!!"#"$""#"!!"!!#"!!#!!!"!"""!!""%#"$#"$"#"!!!"!!!!!"!!!"!"!"!$#%&%%$"""""""!#"!"!!""##"$!!!!!!!$$!!!!!#!!"!!!!%!"$"!!"""!!!!!!!"!!!!!!$$#"!"!!!"!$$#"!$!!!""!"""

    Even after using Falcon-formatter for fasta format conversion, it does NOT work in Falcon.

    And I know that the fasta files require strict formatting with the information of movie, time of run start, SMRT barcode, etc. and should look like this:
    >m140913_050931_42139_c100713652400000001823152404301535_s1_p0/9/1607_26058 RQ=0.831
    TGGCATCTCATAAAGCCGCGCGGACGGGCAATAGCACTGGTTCGATTGTCTGGTGTTTATTCCCGGCTGT
    TGGGCTGAGTTTGTGATCCCGGTGAACTTCTCGCATGCCGACAGCATCATGATCGGTGCGCTGTCTCCCT
    GGCAAATAGAAGTTGTTCAATAACGCGCGCGACTGGCCGTTGGCCTCGGGCGGTTAGCGATGCATCGATG
    TTTGCTGGGCTGCTAATTGTGCCCGATAATATGGTTGGTTCGGCACTAAACGACCAGCAAAAAAAAGCGT
    GGGAGAACAGATGAAATTATTTACGCGGTAGTTCGTTTCGCCGCTGGCGGATTGTGATTTTGCTGGCTTG
    GTCTTACCGTTTTCCTCTACGCGGCCCAATGCTGAGCTGGGTATCTATTCGTTATACGGCTCTGAAGGCT

    My question:

    1. Can I make up some dummy variables equivalent for ">m140913_050931_42139_c100713652400000001823152404301535_s1_p0/9/1607_26058" to make Falcon work properly?

    2. Or is there another way to recover *.sra file I downloaded to make it work properly in Falcon? I downloaded *.sra and then do fastq-dump.
    Does this process lead to the loss of the head information such as "m140913_050931_42139_c100713652400000001823152404301535_s1_p0/9"?

    Looking forward to your help!

    Many thanks!

  • #2
    I was going to point you to http://www.ebi.ac.uk/ena/data/view/SRR1168519 and suggest downloading the 'Submitted files (ftp)', but there are none. I have two alternative solutions left:

    - try to contact the original submitters and ask them for the file(s) they uploaded
    - reverse engineer the names with some fake information that makes the IDs it compatible with FALCON (this requires some scripting)

    Finally, I don't think you are the only one with this problem. I was going to suggest you file an issue on the FALON github pages, but I see you already have https://github.com/PacificBiosciences/FALCON/issues/428 :-)

    Comment


    • #3
      If you click on the Download tab for these runs (example in link) then the "bas.h5" files as submitted are available. If you have access to SMRTportal you may be able to do something with them (though you may still need to create the metadata files).

      Comment


      • #4
        Nice, @GenoMax, I didn't know about that. Now if only ENA would add that link...

        Comment


        • #5
          I got quite a long way with this script:

          I previously encountered a problem (described in #249) where I could not assemble reads that had been error-corrected with PBcR-MHAP because they had had their names changed, and FALCON could not a...


          Also had to remove duplicates

          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
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X