trimming illumina reads

[empyrean]

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

[mgogol]

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_trimmer_usage

looks like you'd want -l 100

[maubp]

Duplicate: http://biostar.stackexchange.com/que...end-fastq-file

[ECO]

Duplicate: http://biostar.stackexchange.com/que...end-fastq-file

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...?

[volks]

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

[tonybolger]

Blatant plug: Trimmomatic, you know it makes sense