Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problem converting solid2fastq with Barcode

    Hi NGS users,
    I always use solid2fastq 0.6.4e (from bfast+bwa-0.6.4e) to convert csfasta2fastq (both single read and paired end) in this way:

    > solid2fastq -o output -b sample_F3.csfasta sample_F5-P2.csfasta sample_F3_QV.qual sample_F5-P2_QV.qual

    and it's run perfectly, generating two file (output.read1.fastq and output.read2.fastq)

    Now, I have SOLiD samples in PE with barcode.
    But when I run

    > solid2fastq -o output -b sample_F3_1_23.csfasta sample_F5-BC_1_23.csfasta sample_F3_QV_1_23.qual sample_F5-BC_QV_1_23.qual

    the program returns me only a single fastq containing only the reads of F5-BC strands. (output.single.fastq)

    How can I fix this problem?
    Thanx a lot,
    ME

  • #2
    Originally posted by m_elena_bioinfo View Post
    Hi NGS users,
    I always use solid2fastq 0.6.4e (from bfast+bwa-0.6.4e) to convert csfasta2fastq (both single read and paired end) in this way:

    > solid2fastq -o output -b sample_F3.csfasta sample_F5-P2.csfasta sample_F3_QV.qual sample_F5-P2_QV.qual

    and it's run perfectly, generating two file (output.read1.fastq and output.read2.fastq)

    Now, I have SOLiD samples in PE with barcode.
    But when I run

    > solid2fastq -o output -b sample_F3_1_23.csfasta sample_F5-BC_1_23.csfasta sample_F3_QV_1_23.qual sample_F5-BC_QV_1_23.qual

    the program returns me only a single fastq containing only the reads of F5-BC strands. (output.single.fastq)

    How can I fix this problem?
    Thanx a lot,
    ME
    Post your question to [email protected] and give the first few reads in both files.

    Comment


    • #3
      I posted the question to bfast-help.
      These are the reads:

      F3_BC.csfasta
      >2_62_1595_F3
      T33222032200312120022000320022021022000022220300200
      >2_63_675_F3
      T30223332233222011120303002321220022222232022302223
      >2_63_759_F3
      T32122302231212321122320322300021031021022202310221
      >2_63_1203_F3
      T30223300233110010221001112211102131021221222302121
      >2_63_1334_F3
      T03011300002002020011000212002210033200100001000010
      >2_63_1841_F3
      T32222332201222021030202202122222222221212222202022
      >2_63_1868_F3
      T30222102221322320120102022020220101222020220002020

      F3_BC_QV
      >2_62_1595_F3
      8 11 15 11 7 5 4 6 4 13 4 4 7 9 22 4 7 5 5 8 11 4 10 4 4 4 4 12 4 18 4 5 7 14 4 6 4 4 4 12 9 5 7 11 4 10 11 8 6 16
      >2_63_675_F3
      21 5 5 5 5 9 4 7 10 6 4 6 5 9 6 5 4 8 4 5 12 7 5 6 4 23 6 5 4 7 14 11 4 17 9 8 11 10 8 6 17 8 10 7 4 6 12 9 5 5
      >2_63_759_F3
      24 4 4 10 9 12 5 4 7 4 7 6 10 10 6 5 4 8 13 4 5 11 5 6 11 19 10 5 5 4 7 4 5 16 8 9 15 10 5 6 13 8 4 5 12 7 13 8 16 13
      >2_63_1203_F3
      18 4 4 16 9 5 6 6 11 4 16 5 4 4 4 20 6 13 26 4 4 8 8 6 13 17 10 27 17 8 6 15 20 7 8 12 20 19 18 8 8 14 4 4 7 5 5 6 25 19
      >2_63_1334_F3
      19 30 24 20 21 23 18 28 27 27 16 24 26 13 4 4 20 22 7 5 16 4 23 15 8 19 14 4 19 7 16 6 16 4 5 5 9 15 9 8 5 8 13 7 4 13 16 5 4 8
      >2_63_1841_F3
      6 4 4 8 5 4 4 4 10 4 12 4 5 10 4 4 4 4 4 4 4 5 7 4 4 12 4 11 7 5 6 4 4 8 11 5 13 6 12 4 4 10 5 9 5 5 7 4 7 8


      F5-BC.csfasta
      >2_62_1595_F5-BC
      G0200102100000300030000103
      >2_63_675_F5-BC
      G0210222100220203000013012
      >2_63_759_F5-BC
      G0200112101000213220022013
      >2_63_1203_F5-BC
      G2200102210020023030013003
      >2_63_1334_F5-BC
      G0002122002220021030000000
      >2_63_1841_F5-BC
      G0222112122230212203020122

      F5-BC_QV
      >2_62_1595_F5-BC
      9 5 4 21 7 5 5 6 7 19 19 11 18 4 5 5 14 10 19 8 12 5 20 4 19
      >2_63_675_F5-BC
      4 25 14 13 8 6 10 7 6 5 4 7 17 4 6 14 11 8 4 10 6 4 9 15 5
      >2_63_759_F5-BC
      7 31 6 6 18 9 5 10 7 9 6 17 5 5 18 5 4 4 9 4 5 4 10 10 4
      >2_63_1203_F5-BC
      14 14 8 20 11 10 14 4 5 4 5 5 21 19 6 5 22 15 21 24 18 4 8 8 15
      >2_63_1334_F5-BC
      5 20 5 9 11 7 32 6 4 4 4 14 18 7 8 4 6 8 14 9 7 14 10 12 11

      Comment


      • #4
        any progress on this?

        Comment


        • #5
          I don't really see why you have to enter both pairs in a single solid2fastq run, since each pair will output a single fastq file. or does solid2fastq perform any kind of extra check when entering single or paired-end data? wouldn't it be easier to call them separately, ie
          Code:
          solid2fastq -o output sample_F3.csfasta sample_F3_QV.qual
          solid2fastq -o output sample_F5-P2.csfasta sample_F5-P2_QV.qual
          I also used to use solid2fastq v0.6.4 to convert my SOLiD output, but I never saw that "-b" option, nor even in the current v0.6.5. did it work for you? what exactly was it doing?

          Comment


          • #6
            Originally posted by Jorge Amigo View Post
            I don't really see why you have to enter both pairs in a single solid2fastq run, since each pair will output a single fastq file. or does solid2fastq perform any kind of extra check when entering single or paired-end data? wouldn't it be easier to call them separately, ie
            Code:
            solid2fastq -o output sample_F3.csfasta sample_F3_QV.qual
            solid2fastq -o output sample_F5-P2.csfasta sample_F5-P2_QV.qual
            I also used to use solid2fastq v0.6.4 to convert my SOLiD output, but I never saw that "-b" option, nor even in the current v0.6.5. did it work for you? what exactly was it doing?
            The "-b" option is in the bfast+bwa-0.6.4e version.

            Comment


            • #7
              Hi I have bwa-0.5.9/solid2fastq.pl version. I have two files SolF3.csfasta & SolF3_QV.qual which i want to convert in 'fastq'. After running the command as :

              perl solid2fastq.pl Sol SolTest

              I am getting the file SolTest.single.fastq.gz but with no reads in file after i unzip it, whereas i have good and equivalent amount of reads in my input read (*F3.csfasta) and qual (*F3_QV.qual) file. Can someone explain me the reason if ever stuck in similar problem.


              Strange to say the same command is working fine with another set of file.

              Comment


              • #8
                this thread was about using solid2fastq with barcodes, so I would suggest you to open a new thread asking for help. in it, I guess the first thing you would be noticed is that it is much faster to use the C implementation of solid2fastq rather than the perl script, and that the typical usage command would be something like this:
                Code:
                solid2fastq -o SolF3 SolF3.csfasta SolF3_QV.qual
                which would generate a SolF3.fastq file with all SolF3 reads with their corresponding qualities.

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Exploring the Dynamics of the Tumor Microenvironment
                  by seqadmin




                  The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                  07-08-2024, 03:19 PM
                • seqadmin
                  Exploring Human Diversity Through Large-Scale Omics
                  by seqadmin


                  In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                  06-25-2024, 06:43 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Today, 07:20 AM
                0 responses
                16 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-16-2024, 05:49 AM
                0 responses
                35 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-15-2024, 06:53 AM
                0 responses
                39 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 07-10-2024, 07:30 AM
                0 responses
                41 views
                0 likes
                Last Post seqadmin  
                Working...
                X