Hello folks, I´m trying to run tophat on some 27bp single end illumina reads with a reference GTF for searching splice junctions.
My mapping reference is just the chr14 and so is the GTF that I retrieved from UCSC genome browser.
The problem is that in despite of not showing any errors in the log files, my *.bed output with the junctions is always empty!! So I´m in doubt if there is something wrong of if there really wasn´t any output what I find a little odd bacause of the long time it took to try to align the reads with the junctions. Take a look at the log file of the output:
Aparently it´s ok, but if I look to the junctions.bed it´s shows only the title:
Please help, tophat parameters are default, i just changed the -p option to use all the cpus of my machine.
Thanks,
Halian
My mapping reference is just the chr14 and so is the GTF that I retrieved from UCSC genome browser.
The problem is that in despite of not showing any errors in the log files, my *.bed output with the junctions is always empty!! So I´m in doubt if there is something wrong of if there really wasn´t any output what I find a little odd bacause of the long time it took to try to align the reads with the junctions. Take a look at the log file of the output:
Code:
[Fri Nov 26 08:19:34 2010] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Fri Nov 26 08:19:34 2010] Preparing output location /usr/local/tophat// [Fri Nov 26 08:19:34 2010] Checking for Bowtie index files [Fri Nov 26 08:19:34 2010] Checking for reference FASTA file [Fri Nov 26 08:19:34 2010] Checking for Bowtie Bowtie version: 0.12.7.0 [Fri Nov 26 08:19:34 2010] Checking for Samtools Samtools version: 0.1.11.0 [Fri Nov 26 08:19:34 2010] Checking reads min read length: 27bp, max read length: 27bp format: fastq quality scale: phred33 (default) [Fri Nov 26 08:21:25 2010] Reading known junctions from GTF file [Fri Nov 26 08:21:49 2010] Mapping reads against chr14.ucsc with Bowtie [Fri Nov 26 08:26:23 2010] Joining segment hits [Fri Nov 26 08:29:13 2010] Mapping reads against chr14.ucsc with Bowtie(1/3) [Fri Nov 26 08:34:02 2010] Mapping reads against chr14.ucsc with Bowtie(2/3) [Fri Nov 26 08:38:43 2010] Mapping reads against chr14.ucsc with Bowtie(3/3) [Fri Nov 26 08:43:27 2010] Searching for junctions via segment mapping [Fri Nov 26 08:43:31 2010] Retrieving sequences for splices [Fri Nov 26 08:43:35 2010] Indexing splices [Fri Nov 26 08:43:35 2010] Mapping reads against segment_juncs with Bowtie [Fri Nov 26 09:59:20 2010] Mapping reads against segment_juncs with Bowtie [Fri Nov 26 11:11:12 2010] Mapping reads against segment_juncs with Bowtie [Fri Nov 26 12:25:22 2010] Joining segment hits [Fri Nov 26 12:31:28 2010] Reporting output tracks ----------------------------------------------- Run complete [04:12:35 elapsed]
Code:
track name=junctions description="TopHat junctions"
Please help, tophat parameters are default, i just changed the -p option to use all the cpus of my machine.
Thanks,
Halian
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