Tophat error( sequence and quality are inconsistent)

[younko]

Hello,

I am trying to map my paried end fastq file to the reference..
I have several samples generated from same library..

However, while I'm mapping the reads to the reference, one of my sample got an error.. I have no idea what I have to do with this since other samples are oaky..

I used the following command.. Could you please give some comments for this?


> tophat -p 8 -G genes.gtf -o KKS_thout --no-novel-juncs genome KKS_R1_1.fq KKS_R1_2.fq

[blancha]

You should really post the error message,when asking for the meaning of an error message.

[younko]

oops sorry.. I meant to put it to the title..

When I check the tophat.log file

while it is prining...

[2014-05-28 16:47:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2014-05-28 16:48:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)


Then it shows...

Parse error at line 78832: sequence and quality are inconsistent

I don;t know why i got this message. since other samples were okay.. which is the exactly same format...

[blancha]

I would check the 2 FASTQ files.
If you transferred the files from another server, for example, and the transfer was incomplete, you could get this type of error message. Just a possibility.