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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Originally posted by KevinLam View PostHi
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.
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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.
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