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Hello,
I am running Tophat with the --GFF option, where I supply it with the GFF of all the genes in my genome so that it can use those existing junctions in addition to discovering novel ones.
Two questions:
1. After the Tophat run, how can I check that Tophat actually used the junctions I gave it? Is there a .log file I can check? I cannot seem to find anything about the status of those junctions in "run.log".
The output I get from Tophat to stdout/stderr is:
[Sat Jul 31 13:22:53 2010] Preparing output location
[Sat Jul 31 13:22:53 2010] Checking for Bowtie index files
[Sat Jul 31 13:22:53 2010] Checking for reference FASTA file
[Sat Jul 31 13:22:53 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Sat Jul 31 13:22:53 2010] Checking reads
seed length: 35bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Sat Jul 31 13:28:28 2010] Mapping reads against mm9_bowtie with Bowtie
[Sat Jul 31 13:45:16 2010] Joining segment hits
[Sat Jul 31 13:48:01 2010] Mapping reads against mm9_bowtie with Bowtie
[Sat Jul 31 14:04:14 2010] Joining segment hits
[Sat Jul 31 14:06:48 2010] Searching for junctions via segment mapping
[Sat Jul 31 15:29:04 2010] Retrieving sequences for splices
[Sat Jul 31 15:30:50 2010] Indexing splices
[Sat Jul 31 15:50:54 2010] Mapping reads against segment_juncs with Bowtie
[Sat Jul 31 16:00:35 2010] Joining segment hits
[Sat Jul 31 16:02:58 2010] Mapping reads against segment_juncs with Bowtie
[Sat Jul 31 16:12:46 2010] Joining segment hits
[Sat Jul 31 16:15:08 2010] Reporting output tracks
Is it supposed to say something about reading junctions from the GFF file here?
2. Finally, when I looked at my Tophat .sam output, it does not contain a header. How can I get Tophat to output the SAM header?
Thanks.
I am running Tophat with the --GFF option, where I supply it with the GFF of all the genes in my genome so that it can use those existing junctions in addition to discovering novel ones.
Two questions:
1. After the Tophat run, how can I check that Tophat actually used the junctions I gave it? Is there a .log file I can check? I cannot seem to find anything about the status of those junctions in "run.log".
The output I get from Tophat to stdout/stderr is:
[Sat Jul 31 13:22:53 2010] Preparing output location
[Sat Jul 31 13:22:53 2010] Checking for Bowtie index files
[Sat Jul 31 13:22:53 2010] Checking for reference FASTA file
[Sat Jul 31 13:22:53 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Sat Jul 31 13:22:53 2010] Checking reads
seed length: 35bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Sat Jul 31 13:28:28 2010] Mapping reads against mm9_bowtie with Bowtie
[Sat Jul 31 13:45:16 2010] Joining segment hits
[Sat Jul 31 13:48:01 2010] Mapping reads against mm9_bowtie with Bowtie
[Sat Jul 31 14:04:14 2010] Joining segment hits
[Sat Jul 31 14:06:48 2010] Searching for junctions via segment mapping
[Sat Jul 31 15:29:04 2010] Retrieving sequences for splices
[Sat Jul 31 15:30:50 2010] Indexing splices
[Sat Jul 31 15:50:54 2010] Mapping reads against segment_juncs with Bowtie
[Sat Jul 31 16:00:35 2010] Joining segment hits
[Sat Jul 31 16:02:58 2010] Mapping reads against segment_juncs with Bowtie
[Sat Jul 31 16:12:46 2010] Joining segment hits
[Sat Jul 31 16:15:08 2010] Reporting output tracks
Is it supposed to say something about reading junctions from the GFF file here?
2. Finally, when I looked at my Tophat .sam output, it does not contain a header. How can I get Tophat to output the SAM header?
Thanks.
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