Hello!
I was trying to run the CollectRnaSeqMetrics from Picard tools. My command was:
java -Xmx4g -jar picard.jar CollectRnaSeqMetrics \
I=/home/ania/STAR_results/SLX-10113.D701_D505.C80D1ANXX/Aligned.out.sam \
O=/home/ania/mappingQC/1-5.RNA_Metrics \
REF_FLAT=/home/ania/STAR/STAR-2.5.2a/bin/Linux_x86_64/gtf/refFlat.txt \
REFERENCE_SEQUENCE=/home/ania/STAR/STAR-2.5.2a/bin/Linux_x86_64/genome/GRCh38_r85.all.fa \
STRAND_SPECIFICITY=NONE \
RIBOSOMAL_INTERVALS=/home/ania/mappingQC/gencode.v19.rRNA.interval_list \
CHART_OUTPUT=/home/ania/mappingQC/file.rnaseq.pdf
I created Ribosomal_intervals file using this script: https://gist.github.com/slowkow/b11c28796508f03cdf4b and making a few changes in it, namely: I changed hg19 to hg38 and gene_type to transcript_biotype
For mapping I used the STAR tool.
Unfortunatelly, what I get is an error:
Exception in thread "main" picard.PicardException: Sequence dictionaries differ in /home/ania/STAR_results/SLX-10113.D701_D505.C80D1ANXX/Aligned.out.sam and /home/ania/mappingQC/gencode.v19.rRNA.interval_list
Together with many warnings like these:
WARNING 2016-07-27 11:06:36 IntervalList Ignoring interval for unknown reference: 13:60613608-60613734 + ENST00000411144
WARNING 2016-07-27 11:06:36 IntervalList Ignoring interval for unknown reference: Y:18348035-18348147 - ENST00000516858
Such warnings refere to all chromosomes.
I'm new to RNA-seq and don't know what to do with this problem. Could you please tell me how I can solve this? I would be extremely grateful.