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csfasta quality hard trimming do i need to hard trim the qual file?

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  • csfasta quality hard trimming do i need to hard trim the qual file?

    Hi
    I need to hard trim 10 bases off the csfasta file and I tried to do the hard trim and quality filter in one step (with the csfasta quality file perl script from solid denovo acc tools)

    but I ended up with a filtered csfasta file only with the qual file still as it is.

    this is a pain for downstream analysis if i have to convert the filtered csfasta into fastq (with the unaltered qual file)

    is there a script that outputs filtered qual file and csfasta in one step?

    (failing which I probably have to do the hard trim on csfasta and qual) then do the quality filter.
    or write my own script for this.
    http://kevin-gattaca.blogspot.com/

  • #2
    Originally posted by KevinLam View Post
    Hi
    I need to hard trim 10 bases off the csfasta file and I tried to do the hard trim and quality filter in one step (with the csfasta quality file perl script from solid denovo acc tools)

    but I ended up with a filtered csfasta file only with the qual file still as it is.

    this is a pain for downstream analysis if i have to convert the filtered csfasta into fastq (with the unaltered qual file)

    is there a script that outputs filtered qual file and csfasta in one step?

    (failing which I probably have to do the hard trim on csfasta and qual) then do the quality filter.
    or write my own script for this.
    The "solid2fastq" program included in the BFAST distribution will allow you to convert CSFASTA/QUAL to FASTQ and trim ("-t INT") from the 3' end of the reads at the same time. You can then use BFAST to align the data .

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    • #3
      Google "rutgers solid filter". It outputs an updated QV.qual file by default.

      I believe the -t and -u options of that script will do what you need, but you'll need to turn off all the other quality-filtering options.

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