Hi everybody,
I am running the tophat2 command like that:
After indexing the fastA file with bowtie2.
It all runs perfectly well and I have now a bam file from the calculations as well as the junctions and indel files.
short background information:
To imitate a circular genome of the mitochondria, I added 500 bases at the end.
With that I can try to identify PE reads which mapped at the "end" of the circular genome, where the second of the pair is mapped at the "beginning" of the chromosome.
I wanted to upload the bam file onto igv, but each time I get an error message.
Has anyone encountered this problem too?
What is the meaning of it?
I have the feeling, that this has something to do with the additional 500 bases at the end, so that some of the reads map as an overhang of the circular genome.
Is there a way to find this kind of mapping?
I would appreciate ant help or ideas.
Assa
I am running the tophat2 command like that:
Code:
tophat2 -p 4 -r 500 -o OUT_DIR chromosome.MT.fa R1.fastq R2.fastq
It all runs perfectly well and I have now a bam file from the calculations as well as the junctions and indel files.
short background information:
To imitate a circular genome of the mitochondria, I added 500 bases at the end.
With that I can try to identify PE reads which mapped at the "end" of the circular genome, where the second of the pair is mapped at the "beginning" of the chromosome.
I wanted to upload the bam file onto igv, but each time I get an error message.
Code:
INFO [2012-09-24 13:48:04,624] [DirectoryManager.java:149] [main] IGV Directory: /home/USER/igv INFO [2012-09-24 13:48:04,630] [Main.java:77] [main] Startup IGV Version 2.1.24 (2563)09/13/2012 09:23 AM Fetching user directory... INFO [2012-09-24 13:48:04,798] [Main.java:78] [main] Default User Directory: /home/USER INFO [2012-09-24 13:48:07,106] [GenomeManager.java:101] [main] Loading genome: genomes/Mus_musculus.MT.500add.fa INFO [2012-09-24 13:48:07,116] [GenomeManager.java:181] [main] Genome loaded. id= Mus_musculus.MT.500add.fa INFO [2012-09-24 13:48:07,311] [CommandListener.java:78] [Thread-6] Listening on port 60151 INFO [2012-09-24 13:48:28,107] [IGV.java:1455] [pool-1-thread-1] Loading1 resources. INFO [2012-09-24 13:49:05,210] [IGV.java:1455] [pool-1-thread-3] Loading1 resources. ERROR [2012-09-24 13:49:05,747] [CachingQueryReader.java:392] [pool-1-thread-4] Error loading alignment data java.lang.ArrayIndexOutOfBoundsException at org.broad.igv.feature.genome.SequenceHelper.getSequence(SequenceHelper.java:164) at org.broad.igv.feature.genome.GenomeImpl.getSequence(GenomeImpl.java:356) at org.broad.igv.sam.BisulfiteCounts.incrementCounts(BisulfiteCounts.java:51) at org.broad.igv.sam.BaseAlignmentCounts.incCounts(BaseAlignmentCounts.java:74) at org.broad.igv.sam.CachingQueryReader$AlignmentTile.addRecord(CachingQueryReader.java:602) at org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:327) at org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:218) at org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:140) at org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:319) at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:54) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:679)
What is the meaning of it?
I have the feeling, that this has something to do with the additional 500 bases at the end, so that some of the reads map as an overhang of the circular genome.
Is there a way to find this kind of mapping?
I would appreciate ant help or ideas.
Assa
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