Hi all,
I ran TopHat, it aligned reads but couldn't find any junctions! So I received files with left-hand reads and right-hand reads (around 30 mln reads) , but the junction database is empy. What can be the problem?
Command line:
/home/programs/tophat/bin/tophat -r 200 -p 8 -o tophatout-11-3 --segment-length 24 --keep-tmp /home/genomes/bowtie/hg19 SRR027870_1.fastq SRR027870_2.fastq
Reads length is 45 bp, I tried to use --segment-reads 24 as mentioned in previous threads, but no effect.
Here is some information:
File segment_junc:
segment_juncs v1.1.2 (exported)
---------------------------
Loading reference sequences...
Loading ...done
Loading left segment hits... Processed 500000 root segment groups
Microaligned 0 segments
done.
Loading right segment hits... Processed 500000 root segment groups
Processed 1000000 root segment groups
Processed 1500000 root segment groups
Microaligned 0 segments
done.
Found 0 potential split-segment junctions
Indexing extensions in /tophatout-11-3/tmp/left_kept_reads_seg1_missing.fq
Indexing extensions in /tophatout-11-3/tmp/left_kept_reads_seg2_missing.fq
Indexing extensions in /tophatout-11-3/tmp/right_kept_reads_seg1_missing.fq
Indexing extensions in /tophatout-11-3/tmp/right_kept_reads_seg2_missing.fq
Total extensions: 72218724
Total extensions: 72218724
Total extensions: 72218724
Total extensions: 72218724
Looking for junctions by island end pairings
Adding hits from segment file 0 to coverage map
Adding hits from segment file 1 to coverage map
Adding hits from segment file 2 to coverage map
Adding hits from segment file 3 to coverage map
Map covers 31687325 bases
Map covers 30905855 bases in sufficiently long segments
Map contains 777008 good islands
38604205 are left looking bases
38603996 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Found 0 potential island-end pairing junctions
done
-- seg --
-- done --
-- cov --
-- done --
-- buf --
-- done --
Reporting potential splice junctions...done
Reported 0 total possible splices
Report from TopHat:
[Wed Jan 12 12:59:35 2011] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Wed Jan 12 12:59:35 2011] Preparing output location /tophatout-11-3/
[Wed Jan 12 12:59:35 2011] Checking for Bowtie index files
[Wed Jan 12 12:59:35 2011] Checking for reference FASTA file
[Wed Jan 12 12:59:35 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jan 12 12:59:36 2011] Checking for Samtools
Samtools version: 0.1.10.0
[Wed Jan 12 13:00:41 2011] Checking reads
min read length: 45bp, max read length: 45bp
format: fastq
quality scale: phred33 (default)
[Wed Jan 12 13:06:58 2011] Mapping reads against hg19 with Bowtie
[Wed Jan 12 13:18:52 2011] Joining segment hits
[Wed Jan 12 13:21:33 2011] Mapping reads against hg19 with Bowtie(1/2)
[Wed Jan 12 13:25:00 2011] Mapping reads against hg19 with Bowtie(2/2)
[Wed Jan 12 13:29:56 2011] Mapping reads against hg19 with Bowtie
[Wed Jan 12 13:41:14 2011] Joining segment hits
[Wed Jan 12 13:43:53 2011] Mapping reads against hg19 with Bowtie(1/2)
[Wed Jan 12 13:48:26 2011] Mapping reads against hg19 with Bowtie(2/2)
[Wed Jan 12 13:55:16 2011] Searching for junctions via segment mapping
Warning: junction database is empty!
[Wed Jan 12 13:58:43 2011] Joining segment hits
[Wed Jan 12 14:01:41 2011] Joining segment hits
[Wed Jan 12 14:04:35 2011] Reporting output tracks
-----------------------------------------------
Run complete [01:19:07 elapsed]
Any help is very appreciated!
I ran TopHat, it aligned reads but couldn't find any junctions! So I received files with left-hand reads and right-hand reads (around 30 mln reads) , but the junction database is empy. What can be the problem?
Command line:
/home/programs/tophat/bin/tophat -r 200 -p 8 -o tophatout-11-3 --segment-length 24 --keep-tmp /home/genomes/bowtie/hg19 SRR027870_1.fastq SRR027870_2.fastq
Reads length is 45 bp, I tried to use --segment-reads 24 as mentioned in previous threads, but no effect.
Here is some information:
File segment_junc:
segment_juncs v1.1.2 (exported)
---------------------------
Loading reference sequences...
Loading ...done
Loading left segment hits... Processed 500000 root segment groups
Microaligned 0 segments
done.
Loading right segment hits... Processed 500000 root segment groups
Processed 1000000 root segment groups
Processed 1500000 root segment groups
Microaligned 0 segments
done.
Found 0 potential split-segment junctions
Indexing extensions in /tophatout-11-3/tmp/left_kept_reads_seg1_missing.fq
Indexing extensions in /tophatout-11-3/tmp/left_kept_reads_seg2_missing.fq
Indexing extensions in /tophatout-11-3/tmp/right_kept_reads_seg1_missing.fq
Indexing extensions in /tophatout-11-3/tmp/right_kept_reads_seg2_missing.fq
Total extensions: 72218724
Total extensions: 72218724
Total extensions: 72218724
Total extensions: 72218724
Looking for junctions by island end pairings
Adding hits from segment file 0 to coverage map
Adding hits from segment file 1 to coverage map
Adding hits from segment file 2 to coverage map
Adding hits from segment file 3 to coverage map
Map covers 31687325 bases
Map covers 30905855 bases in sufficiently long segments
Map contains 777008 good islands
38604205 are left looking bases
38603996 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Found 0 potential island-end pairing junctions
done
-- seg --
-- done --
-- cov --
-- done --
-- buf --
-- done --
Reporting potential splice junctions...done
Reported 0 total possible splices
Report from TopHat:
[Wed Jan 12 12:59:35 2011] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Wed Jan 12 12:59:35 2011] Preparing output location /tophatout-11-3/
[Wed Jan 12 12:59:35 2011] Checking for Bowtie index files
[Wed Jan 12 12:59:35 2011] Checking for reference FASTA file
[Wed Jan 12 12:59:35 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Jan 12 12:59:36 2011] Checking for Samtools
Samtools version: 0.1.10.0
[Wed Jan 12 13:00:41 2011] Checking reads
min read length: 45bp, max read length: 45bp
format: fastq
quality scale: phred33 (default)
[Wed Jan 12 13:06:58 2011] Mapping reads against hg19 with Bowtie
[Wed Jan 12 13:18:52 2011] Joining segment hits
[Wed Jan 12 13:21:33 2011] Mapping reads against hg19 with Bowtie(1/2)
[Wed Jan 12 13:25:00 2011] Mapping reads against hg19 with Bowtie(2/2)
[Wed Jan 12 13:29:56 2011] Mapping reads against hg19 with Bowtie
[Wed Jan 12 13:41:14 2011] Joining segment hits
[Wed Jan 12 13:43:53 2011] Mapping reads against hg19 with Bowtie(1/2)
[Wed Jan 12 13:48:26 2011] Mapping reads against hg19 with Bowtie(2/2)
[Wed Jan 12 13:55:16 2011] Searching for junctions via segment mapping
Warning: junction database is empty!
[Wed Jan 12 13:58:43 2011] Joining segment hits
[Wed Jan 12 14:01:41 2011] Joining segment hits
[Wed Jan 12 14:04:35 2011] Reporting output tracks
-----------------------------------------------
Run complete [01:19:07 elapsed]
Any help is very appreciated!
Comment