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Old 12-12-2011, 02:23 PM   #4
Wallysb01
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Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286
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Quote:
Originally Posted by marb View Post
Do you think about header of bam file?
I obtained 28 fastq files from Casava - 14 right-end (R1) 14 left-end (R2).
I have processed them by tophat.
Are you sure tophat used them as paired and not singled? How do the ends of your sequence headers look in the fastq format? If they come out with:

@XXXX 1:N:0 @XXXX 2:N:0
AGC.. GCT
+XXXX 1:N:0 +XXXX 1:N:0
.... .....

a lot of programs won't recognize that as paired end files. You need to convert it to:

@XXXX/1 @XXXX/2
AGC.. GCT
+XXXX/1 +XXXX/2
.... .....

I came on here with the same kinds of issues and a friendly commenter made this post to help people like me out:

http://contig.wordpress.com/2011/09/...-fastq-header/
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