SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to handle Ns in the middle of reads themysticgeek Bioinformatics 4 01-20-2014 04:27 AM
TopHat doesnt handle 450million reads EBER Bioinformatics 2 05-25-2012 05:09 AM
TopHat 1.1 failing on colorspace SE reads krobison Bioinformatics 22 09-22-2011 11:25 AM
how does bowtie handle n's in reads? ref sequence? nashp Bioinformatics 0 01-10-2011 04:09 PM
BWA mapping colorspace reads Todd Scheetz SOLiD 2 08-25-2010 06:16 PM

Reply
 
Thread Tools
Old 01-03-2015, 02:19 AM   #1
Fernas
Member
 
Location: Middle East

Join Date: Apr 2013
Posts: 74
Default Can Trimmomatic handle Colorspace Reads

I have a RNASeq fastq file (first 4 lines are):
=====
@SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
T.33.2010.0313.1231222320.1.3312.0.12.0212.0.013000
+SRR179591.1.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_58_235_F3 length=50
!!A+!@>A5!@59%!=A'6=4@5'A!9!55=1!(!0-!'%-%!&!%&%60'
=====

This fastq format is Color-space. I am wondering if Trimmomatic can handle such file by trimming reads based on quality and adapters?
(I did not see in the documentation of Trimmomatic that it can handle Color-space reads).
Fernas is offline   Reply With Quote
Old 01-03-2015, 03:42 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,885
Default

You will need to use Cutadapt: https://code.google.com/p/cutadapt/
GenoMax is offline   Reply With Quote
Old 01-03-2015, 04:13 AM   #3
Fernas
Member
 
Location: Middle East

Join Date: Apr 2013
Posts: 74
Default

Thank @GenoMax.
Actually, I have 100 fastq files. 95 of them contain quality values encoded in Phred33 (so I processed them with Trimmomatic), while 5 files are Color-space. I wanted to use Trimmomatic for all the 100 files for simplicity but it seems that I need to process those 5 files with Cutadapt.
Fernas is offline   Reply With Quote
Old 01-03-2015, 06:04 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,885
Default

If you are worried about consistency then you could re-process them all with cutadapt.
GenoMax is offline   Reply With Quote
Reply

Tags
color space, trimmomatic

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:39 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO