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program which can make a pair end to have equal number of sequence

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  • program which can make a pair end to have equal number of sequence

    i have a PE100, the problem is some tiles of read 2 are corrupted and it caused un even number of reads in read 1 and read 2. Are there any programs which can match up sequences from both reads and just keep mathed ones for down stream analysis. Thanks

    mike

  • #2
    re-pairing PE files

    I remember a nice contribution from kmcarr a while back which can probably help; search for thread 10392. (incidentally I can't recommend my own contribution to that thread - it is hideously slow)

    best

    m
    Last edited by mgg; 02-27-2012, 03:55 AM. Reason: typo correction

    Comment


    • #3
      Originally posted by mgg View Post
      I remember a nice contribution from kmcarr a while back which can probably help; search for thread 10392. (incidentally I can't recommend my own contribution to that thread - it is hideously slow)

      best

      m
      m,

      Thanks for the acknowledgement. Here is a link to the thread. If you go there you'll see that I just posted an update. Due to a limitation in cdbfasta my method will not work for large input fastq files. The only work-around at the moment is to split the input up into smaller chunks.

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      • #4
        The trimmer Trimmomatic outputs files with intact pairs as well as files with single reads. It should be able to split your files in the way you want, as well as do trimming at the same time if you wish.

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        • #5
          I wrote a script exactly to tackle that issue. You'll find a copy attached.
          The script will output either an interleaved mate pair fastq or two fastq files. The unpaired reads will also be saved in a separate file. The script uses a regular expression to identify the ID, so let me know if you need help with that. It requires at least as much RAM as the size of the first file. Feel free to use it and let please let me know how can we improve it.
          Adhemar
          Attached Files

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          • #6
            Maybe of interest as well, PairedreadFinder:
            Usage: PairedreadFinder, Version 1.01. This tool takes two fasta/q files and looks for matching readnames in both files. [OPTION]...

            -h, --help displays this help message
            -v, --version return program version
            -s1, --source1 input file 1
            -s2, --source2 input file 2
            -f, --format input file format
            -t1, --target1 target file 1
            -t2, --target2 target file 2
            -n, --nr-threads nr of threads to use (default 1)
            -is, --suffix-ignore nr of characters to ignore from the END of the readname (in case paired reads are named like /1 /2 it should be set to 2) (default 0)
            -ip, --prefix-ignore nr of characters to ignore from the BEGINNING of the readname (in case paired reads are named like s_1.. s_2.. it should be set to 3) (default 0)
            from FAR, http://sourceforge.net/apps/mediawik...itle=Main_Page

            Sven

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            • #7
              hi azneto, how to setup regular expression like the following
              @HWI-ST829:138071VACXX:1:1101:1131:2048 1:N:0:ATCACG.

              Thanks.

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              • #8
                Hi dejavu2010.

                @HWI-ST829:138071VACXX:1:1101:1131:2048 1:N:0:ATCACG.

                you can use: '^@(\S+)\s[1|2]\S+$'

                Assuming that 1 and 2 will appear right after the space char.
                '@' 'ID' 'space' '1or1' '...'

                I'll add this example to the script.

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                • #9
                  Hi

                  my process got killed

                  perl mergeShuffledFastqSeqs.pl -f1 2044-BH-1_1_sequence.txt -f2 2044-BH-1_2_sequence.txt -r '^@(\S+)\s[1|2]\S+$' -o 2044-BH-1 -t

                  Loading the first file...Killed

                  2044-BH-1_1_sequence.txt 18gb, the other one is 17gb. we have a server with 32 duel core cpus and 192gb mem. I wonder what could be the reason it got killed.

                  thx

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                  • #10
                    Picard has a FixMateInformation to "Ensure that all mate-pair information is in sync between each read and it's mate pair."
                    http://picard.sourceforge.net/comman...ateInformation

                    If you are in Galaxy this is implemented under Picard as: Paired Read Mate Fixer

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                    • #11
                      Hi,
                      It most probably is a memory issue.
                      The script loads only the first file into the memory and starts to match with the entries in the second file. You'll have to monitor the memory usage ('top' or 'free -m').
                      I just ran a test and perl uses 220Gb RAM for two 33Gb fastq file.
                      Soon I'll start to search for alternative ways to handle memory using perl in order to improve the script. I'll let you know.
                      -Adhemar

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                      • #12
                        thx. everybody, i got it resolved

                        thx. everybody, i got it resolved

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                        • #13
                          i feel that Trimmomatic index your reads based on input order, not lane_position_... combination, i tested one un matched dataset, they can not handle it.

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                          • #14
                            Originally posted by kmcarr View Post
                            m,

                            Thanks for the acknowledgement. Here is a link to the thread. If you go there you'll see that I just posted an update. Due to a limitation in cdbfasta my method will not work for large input fastq files. The only work-around at the moment is to split the input up into smaller chunks.
                            The other work-around is to stick with fasta files (smaller index files). If you are mapping to a reference and the quality scores are important then this probably won't help, but for assembly it doesn't matter.

                            Originally posted by sklages View Post
                            Maybe of interest as well, PairedreadFinder:
                            from FAR, http://sourceforge.net/apps/mediawik...itle=Main_Page

                            Sven
                            Has anyone actually used this program and found it to work correctly? I gave it a try but found several bugs. First, it inserted random blank lines in the individual "paired" output files. Second, the individual "paired" files actually differed by more than 800 records with my data, which means that trying to interleave the two files causes them to get all out of order. Of course, this could be due to the data or the user, but I've successfully used other methods with the same data and the usage of the program is quite simple, so I'm a bit skeptical on this one.

                            Comment


                            • #15
                              Hi All,

                              I have exactly this problem as well, but with fasta files. Anybody know of a program that will work with Fasta or could modify 'mergeShuffledFastqSeqs.pl' so it would work on that format as well?

                              Much appreciated.

                              Comment

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