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Re: Quality trimming of fastq file

by Cristoforo (Curate)
on Jan 08, 2018 at 19:44 UTC ( #1206932=note: print w/replies, xml ) Need Help??


in reply to Quality trimming of fastq file

Hi,

What does the input file look like? Are any of these formats in the form that you have?

One problem I see is you are altering an array with pop while iterating over the array and this will likely cause problems.

Your code:

foreach $value (@num_value) { if ($value<$cut_off) { pop(@num_value); + }else{ last; } } $sub1=substr($dna,-@num_value); @qscopy=reverse @num_value; foreach $value (@qscopy) { if ($value<$cut_off) { pop(@qscopy); }else{ last; } }
First you iterate over @num_value popping off elements (wrongly I believe) and then you reverse the array into @gscopy and pop again, (wrongly again I believe), if the amount is less than $cut_off.

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