How to get read group information for bam file

Question

[gskbioinfo143]

Hi I'm trying to compute quality metrics for RNA-seq data using RNA-SeQC software, it is asking for read groups of bam file.

I tried using the command samtools view DGL-104.bam | grep '^@RG' but I'm not getting anything. How do I solve this? Shall I add read groups?

Answer 1

[Devon Ryan]

Try samtools view -H DGL-104.bam | grep '^@RG' instead. If there are no read groups then yes, you'll need to add them (normally one knows if one has already done this).

[gskbioinfo143]

Yes I tried this command too there are no read groups. How to add read groups? Any suggestions?

Thanks

[Devon Ryan]

Picard Tools has an AddOrReplaceReadGroups command.

[gskbioinfo143]

Hey I tried adding read groups and did analysis with RNA-SeQC thre was some output but it showed error as mentioned below

Running GATK Depth of Coverage Analysis ....
Arguments:    -T DepthOfCoverage -R hg19_.fasta -I DGL-reorder-104.bam -o ./testReport//TestId/highexpr//perBaseDoC.out -L ./testReport//TestId/highexpr/intervals.list -l ERROR
Arguments Array:    [-T, DepthOfCoverage, -R, hg19_.fasta, -I, DGL-reorder-104.bam, -o, ./testReport//TestId/highexpr//perBaseDoC.out, -L, ./testReport//TestId/highexpr/intervals.list, -l, ERROR]
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.util.LinkedList.linkLast(LinkedList.java:140)
    at java.util.LinkedList.add(LinkedList.java:336)
    at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState$ReadStateManager.addReadsToSample(LocusIteratorByState.java:762)
    at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState$ReadStateManager.collectPendingReads(LocusIteratorByState.java:700)
    at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.lazyLoadNextAlignmentContext(LocusIteratorByState.java:375)
    at org.broadinstitute.sting.gatk.iterators.LocusIteratorByState.hasNext(LocusIteratorByState.java:345)
    at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:70)
    at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
    at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.advance(WindowMaker.java:168)
    at org.broadinstitute.sting.gatk.executive.WindowMaker$WindowMakerIterator.hasNext(WindowMaker.java:137)
    at org.broadinstitute.sting.gatk.datasources.providers.LocusView.advance(LocusView.java:156)
    at org.broadinstitute.sting.gatk.datasources.providers.LocusView.hasNextLocus(LocusView.java:122)
    at org.broadinstitute.sting.gatk.datasources.providers.AllLocusView.advance(AllLocusView.java:102)
    at org.broadinstitute.sting.gatk.datasources.providers.AllLocusView.hasNext(AllLocusView.java:60)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:50)
    at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:63)
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:248)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
    at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runDoC(GATKTools.java:59)
    at org.broadinstitute.cga.rnaseq.PerBaseDoC.runDoC(PerBaseDoC.java:901)
    at org.broadinstitute.cga.rnaseq.PerBaseDoC.runDoC(PerBaseDoC.java:870)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:271)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:171)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:139)

Please I need suggestion how to solve

Thanks