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Old 06-02-2009, 02:50 PM   #1
joseph
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Location: ca

Join Date: Feb 2008
Posts: 39
Default TopHat: no GFF3_file.expr in the output

Can you please help me to figure out why the “GFF3_file.expr” was not generated without getting any error message?
I had someone made me a GFF3 file from the KnowGene table; the first lines look like this:


##gff-version 3
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4121 0 + 0 ID=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4121 0 + 0 ID=uc001aaa.2mRNA;Parent=uc001aaa.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc001aaa.2exon1;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 2584 0 + 0 ID=uc001aaa.2exon2;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 3083 4121 0 + 0 ID=uc001aaa.2exon3;Parent=uc001aaa.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 1115 4272 0 + 0 ID=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 1115 4272 0 + 0 ID=uc009vip.1mRNA;Parent=uc009vip.1gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 1115 2090 0 + 0 ID=uc009vip.1exon1;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 2475 4272 0 + 0 ID=uc009vip.1exon2;Parent=uc009vip.1mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC gene 4268 14764 0 - 0 ID=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC mRNA 4268 14764 0 - 0 ID=uc001aab.2mRNA;Parent=uc001aab.2gene
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4268 4692 0 - 0 ID=uc001aab.2exon1;Parent=uc001aab.2mRNA
gi|89161185|ref|NC_000001.9|NC_000001 UCSC exon 4832 4901 0 - 0 ID=uc001aab.2exon2;Parent=uc001aab.2mRNA


I ran TopHat with the following command:

tophat -r 200 /myDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7_1.fastq s_7_2.fastq -G GFF3_knownGene
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Old 06-02-2009, 07:19 PM   #2
Cole Trapnell
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Hi Joseph,

All of the options need to be specified before the index and reads in the command. If you run it like this:

tophat -G GFF3_knownGene -r 200 /myDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7_1.fastq s_7_2.fastq

You should get a non-empty .expr file.
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Old 06-03-2009, 08:49 AM   #3
joseph
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Location: ca

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Default Error: Report generation failed

Quote:
Originally Posted by Cole Trapnell View Post
Hi Joseph,

All of the options need to be specified before the index and reads in the command. If you run it like this:

tophat -G GFF3_knownGene -r 200 /myDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7_1.fastq s_7_2.fastq

You should get a non-empty .expr file.
Hi Cole
I still don’t see an .expr file.
Here is the content of tophat_out
ls
GFF3_knownGene.juncs junctions.bed left_kept_reads.fq.candidate_hits.sam right_kept_reads.fq
accepted_hits.sam knownGene.juncs logs right_kept_reads.fq.candidate_hits.sam
coverage.wig left_kept_reads.fq repeat_reads.fa tmp


tophat -G GFF3_knownGene -r 200 /MyDir/bowtie-0.9.9.3/indexes/h_sapiens_asm s_7test_1.fastq s_7test_2.fastq

[Wed Jun 3 09:30:42 2009] Beginning TopHat run (v1.0.8)
-----------------------------------------------
[Wed Jun 3 09:30:42 2009] Preparing output location ./tophat_out/
[Wed Jun 3 09:30:42 2009] Checking for Bowtie index files
[Wed Jun 3 09:30:42 2009] Checking for reference FASTA file
[Wed Jun 3 09:30:42 2009] Checking for Bowtie
Bowtie version: 0.9.9.3
[Wed Jun 3 09:30:42 2009] Checking reads
seed length: 36bp
format: fastq
quality scale: phred
[Wed Jun 3 09:30:42 2009] Reading known junctions from GFF file
Warning: TopHat did not find any junctions in GFF file
Splitting reads into 1 segments
[Wed Jun 3 09:31:01 2009] Mapping reads against h_sapiens_asm with Bowtie
Splitting reads into 1 segments
[Wed Jun 3 09:31:12 2009] Mapping reads against h_sapiens_asm with Bowtie
[Wed Jun 3 09:31:21 2009] Searching for junctions via coverage islands
[Wed Jun 3 09:34:58 2009] Searching for junctions via mate-pair closures
[Wed Jun 3 09:39:55 2009] Retrieving sequences for splices
[Wed Jun 3 09:42:17 2009] Indexing splices
[Wed Jun 3 09:42:17 2009] Mapping reads against segment_juncs with Bowtie
[Wed Jun 3 09:42:18 2009] Joining segment hits
[Wed Jun 3 09:42:18 2009] Mapping reads against segment_juncs with Bowtie
[Wed Jun 3 09:42:18 2009] Joining segment hits
[Wed Jun 3 09:42:18 2009] Reporting output tracks
[FAILED]
Error: Report generation failed
M1-80330:test jdhahbi$
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Old 06-03-2009, 08:54 AM   #4
Cole Trapnell
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Join Date: Nov 2008
Posts: 212
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Can you please email me the logs directory?
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