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Old 12-16-2011, 12:15 PM   #1
empyrean
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Default trimming illumina reads

hi

i have miseq reads of 150 * 2 paired end library. I wanted this to make it look like hiseq library 100bases. is there a way where i can keep only 100 bases in each read and trim the rest at the end to make it a 100 * 2 library?

Thank you
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Old 12-19-2011, 07:10 AM   #2
mgogol
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http://hannonlab.cshl.edu/fastx_tool..._trimmer_usage

looks like you'd want -l 100
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Old 12-19-2011, 08:35 AM   #3
maubp
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Duplicate: http://biostar.stackexchange.com/que...end-fastq-file
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Old 12-19-2011, 08:45 AM   #4
ECO
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Quote:
Originally Posted by maubp View Post
At some point we are going to duplicate Biostar...I haven't thought about how to deal with that, but I think for now it's not "reported post" worthy...?
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Old 12-20-2011, 03:43 PM   #5
volks
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or just use awk:
awk {print substr($1, 1, 100)} reads.fastq

if the ID is line is longer than your desired read length:
awk '{if(NR%4==1){print $1} else{print substr($1, 1, 20)}}' reads.fastq
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Old 12-21-2011, 12:48 AM   #6
tonybolger
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Blatant plug: Trimmomatic, you know it makes sense
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