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Forum: Bioinformatics 09-25-2010, 06:20 AM
Replies: 25
Views: 5,079
Posted By 0xTc0
That is no FastQ format as Tophat correctly...

That is no FastQ format as Tophat correctly complains. FastQ format looks like this:

@SOLEXA2_0827_FC707M4AAXX:5:1:1004:21272
GCTCGGGCAAAATGGTGGACGCCACTCAGGCTGATCTTGN
+...
Forum: Bioinformatics 09-24-2010, 09:38 AM
Replies: 25
Views: 5,079
Posted By 0xTc0
Could you send me the first, 4-8 lines of your...

Could you send me the first, 4-8 lines of your fasta file. Could it be, that
/bowtie-0.12.7/indexes/s_5_sequence.fq

is indexed or so?

Only the reference sequence (hg19) has to be indexed!...
Forum: Bioinformatics 09-24-2010, 02:50 AM
Replies: 25
Views: 5,079
Posted By 0xTc0
Sry if I misunderstood your problem, but would...

Sry if I misunderstood your problem, but would not be the the right command as simply as:

tophat -r 220 /home/johnathon/bowtie-0.12.7/indexes/hg19 ...
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