SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA aligned pairs read1=XT:A:U, read2=XT:A:R jflowers Bioinformatics 1 07-29-2014 10:06 PM
Paired end- search for complement of Read2 in Read1 flacchy Introductions 9 05-23-2013 06:55 AM
refGene.txt sizes and frameshifts of exons not consistent jdenvir Bioinformatics 0 04-09-2013 11:36 AM
Cufflinks FPKM output not consistent with different thread numbers Rachel Hillmer RNA Sequencing 1 07-23-2012 03:27 PM
Current read1, index, and read2 primers for HiSeq2000 SeqVicious Illumina/Solexa 1 09-26-2011 02:12 PM

Reply
 
Thread Tools
Old 07-16-2013, 01:09 AM   #1
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 57
Default Read1 and Read2 are not consistent

Hi, I got the sequencing data from Illumina HiSeq2000. Its pairend sequencing.
The two fastq files(read1 and read2) does not contain equal number of lines.
19166068 read1.fastq
19295372 read2.fastq

Is there any way that I can make them equal by removing the lines which are not there in read1 file?
priya is offline   Reply With Quote
Old 07-16-2013, 01:48 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Yeah, have a look at this thread on Biostars for some example commands. Allegedly, you can also use cmpfastq, which is a perl script, to do this too (I've never used this so I can't say that it works properly).

In the future, use a trimmer that handles both reads of a pair at once so you can avoid these issues.
dpryan is offline   Reply With Quote
Old 07-16-2013, 02:42 AM   #3
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 57
Default

Quote:
Originally Posted by dpryan View Post
Yeah, have a look at this thread on Biostars for some example commands. Allegedly, you can also use cmpfastq, which is a perl script, to do this too (I've never used this so I can't say that it works properly).

In the future, use a trimmer that handles both reads of a pair at once so you can avoid these issues.
Thanks for your reply.I will look into it..
priya is offline   Reply With Quote
Reply

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 06:20 AM.


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