trimming illumina reads

empyrean · 12-16-2011, 12:15 PM

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 · 12-19-2011, 07:10 AM

http://hannonlab.cshl.edu/fastx_tool..._trimmer_usage

looks like you'd want -l 100

maubp · 12-19-2011, 08:35 AM

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

ECO · 12-19-2011, 08:45 AM

Quote:

Originally Posted by maubp

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 · 12-20-2011, 03:43 PM

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 · 12-21-2011, 12:48 AM

Blatant plug: Trimmomatic, you know it makes sense

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12-16-2011, 12:15 PM	#1
empyrean Member Location: EU Join Date: Sep 2010 Posts: 52	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

12-19-2011, 07:10 AM	#2
mgogol Senior Member Location: Kansas City Join Date: Mar 2008 Posts: 197	http://hannonlab.cshl.edu/fastx_tool..._trimmer_usage looks like you'd want -l 100

12-19-2011, 08:35 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Duplicate: http://biostar.stackexchange.com/que...end-fastq-file

12-20-2011, 03:43 PM	#5
volks Member Location: hd.de Join Date: Jun 2010 Posts: 81	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

12-21-2011, 12:48 AM	#6
tonybolger Senior Member Location: berlin Join Date: Feb 2010 Posts: 156	Blatant plug: Trimmomatic, you know it makes sense