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?

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..:)