Originally posted by ohofmann
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Hi Nils
Just wondering can SRMA be used for rescuing orphaned reads. So we have a dataset of variable insert library as we are sequencing the 5' and 3' end of transcripts. As a result the distance between the mates( <--- --->) is dependent on the length of transcript. To map the reads initially I am first using Mosaik which i belv does a better job with variable insert mate pair data.
After mapping we still see 40% orphaned reads where one read maps and the other doesn't. I am wondering if SRMA can rescue these reads.
Thanks!
-Abhi
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Originally posted by ymc View PostDead project now? Are there other alternatives that work on the whole genome?
We have also parallelized the GATK implementation of LR if you are interested. I am not sure which is better at realigning. I do remember comparing SRMA and GATK LR and there are differences but it was not clear to me if one was consistently better than the other. I suspect that Nils would be a better source for info on that.
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Tried several bams with 0.1.16 but all I got was this:
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
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Originally posted by ymc View PostTried several bams with 0.1.16 but all I got was this:
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
at java.util.ArrayList$SubList.add(ArrayList.java:965)
Comment
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I have been interested in this tool for some time but never got it working:
Input is a sorted bam.
java -Xmx16g -jar srma-0.1.15.jar I=491_full_s.bam O=srma_491.bam R=../NC_002516.fna
[Fri Aug 17 10:00:54 CEST 2012] srma.SRMA INPUT=[491_full_s.bam] OUTPUT=[srma_491.bam] REFERENCE=../NC_002516.fna OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/colin2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
java.util.NoSuchElementException
at java.util.Scanner.nextLine(Scanner.java:1503)
at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:131)
at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
at srma.SRMA.doWork(SRMA.java:131)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at srma.SRMA.main(SRMA.java:98)
Please report bugs to [email protected]
The fasta index file looks like this:
more ../NC_002516.fna.fai
NC_002516.2 6264404 58 70 71
Cheers for any help.
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There are thousands of lines of these error messages. If I copy the stderr output, it will be too many lines. You can replicate my problem by downloading the pair-ended reads from
ftp://ftp.1000genomes.ebi.ac.uk/vol1...sequence_read/
and then align them using bwa. I got the same bug with SRR098401_*.filt.fastq.gz and SRR035330_*.filt.fastq.gz
Comment
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Originally posted by colindaven View PostI have been interested in this tool for some time but never got it working:
Input is a sorted bam.
java -Xmx16g -jar srma-0.1.15.jar I=491_full_s.bam O=srma_491.bam R=../NC_002516.fna
[Fri Aug 17 10:00:54 CEST 2012] srma.SRMA INPUT=[491_full_s.bam] OUTPUT=[srma_491.bam] REFERENCE=../NC_002516.fna OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/colin2 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
java.util.NoSuchElementException
at java.util.Scanner.nextLine(Scanner.java:1503)
at net.sf.picard.reference.FastaSequenceIndex.parseIndexFile(FastaSequenceIndex.java:131)
at net.sf.picard.reference.FastaSequenceIndex.<init>(FastaSequenceIndex.java:55)
at net.sf.picard.reference.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:95)
at srma.SRMA.doWork(SRMA.java:131)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at srma.SRMA.main(SRMA.java:98)
Please report bugs to [email protected]
The fasta index file looks like this:
more ../NC_002516.fna.fai
NC_002516.2 6264404 58 70 71
Cheers for any help.
Originally posted by ymc View PostThere are thousands of lines of these error messages. If I copy the stderr output, it will be too many lines. You can replicate my problem by downloading the pair-ended reads from
ftp://ftp.1000genomes.ebi.ac.uk/vol1...sequence_read/
and then align them using bwa. I got the same bug with SRR098401_*.filt.fastq.gz and SRR035330_*.filt.fastq.gz
Comment
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