View Test RNA-SeQC with Hemileia Transcriptome
Map RNA reads to Transcriptome Assembly
bio@ticuna:/data/process/Roya/mapReadsTransToTranscriptome$ clc_ref_assemble_long -d ../RawDataRoya/RNASeqBGI/Results/Paired_Assemby/Hv701_Trans.fasta -q ../RawDataRoya/RNASeqBGI/Hv701_L1_1.fq ../RawDataRoya/RNASeqBGI/Hv701_L1_2.fq -o mapReadsTransToTranscriptome.cas
Convert cas file to bam file
castosam -a mapReadsTransToTranscriptome.cas -o mapReadsTransToTranscriptome.cas.bam
Sort bam file to generate the index file
samtools sort mapReadsTransToTranscriptome.cas.bam mapReadsTransToTranscriptome.cas.bam.sorted
samtools index mapReadsTransToTranscriptome.cas.bam.sorted.bam
Generate .sam to generate .gtf
/opt/cufflinks-1.3.0.Linux_x86_64/cufflinks mapReadsTransToTranscriptome.cas.sorted.bam
Executing RNA-SeQC
bio@ticuna:/data/process/Roya/mapReadsTransToTranscriptome$ java -jar /opt/RNA-SeQC/RNA-SeQC_v1.0.1.jar -n 1000 -s “TestId|mapReadsTransToTranscriptome.cas.bam.sorted.bam|TestDesc” -t transcripts.gtf -r Hv701_Trans.fasta -o ./testReport
Creating rRNA Interval List based on given GTF annotations Retriving contig names from reference contig names in reference: 55791 Loading GTF for Read Counting Converting to refGene Transcript objects to RefGen format: 531 s java.lang.RuntimeException: No rRNA found in GTF transcript_type field at org.broadinstitute.cga.rnaseq.TranscriptList.toRRNAIntervalList(TranscriptList.java:329) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.createRefGeneAndRRNAFiles(RNASeqMetrics.java:955) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:164) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:141) at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:116) RNASeqMetrics Total Runtime: 8 min
Error output, and not exist software documentation.