RNA-SEQ with SOLID reads

[dnyansagar]

Hi
I have Solid reads of length 75 x 35
I want to use Tophat and cufflinks to analyze these reads. But the problem is I dont have the fastq files. I have already mapped reads in BAM format.
should I re-run tophat on these mapped reads? and how?
and which library type I should use? and how ?

/dnyansagar

[paolo.kunder]

Hi,
cufflinks and cuffdiff accepts bam files so you should be able to use your aligned bam files,
anyway I would suggest to align your reads with tophat (-C opton for colour space, fr-secondstrand for SoliD platform)

have a look to the manual, is well documented,

tophat -G reference.gtf -C --library-type fr-secondstrand -o output path_to_bowtie f3.csfasta f5.csfasta

Paolo

[dnyansagar]

Hi
I tried running tophat with above options with only one exception, instead of fasta/fastq I used bam file as input
I got this error
""Error running 'prep_reads'
terminate called after throwing an instance of 'int' ""
what am I doing wrong?

[paolo.kunder]

tophat is used to align reads and to output a bam file, if you have already a bam file why are you using tophat???

[dnyansagar]

Hi
I know that but the bam files I have do not have XS tag info so the cufflinks is not accepting those bam files.
any other solution to the problem?

[paolo.kunder]

I encountered the same problem last year

http://seqanswers.com/forums/showthread.php?t=23108

noone replied me so I realigned reads with Tophat!
paolo