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interval_list for hg38

I was wondering if anyone could help me with this. I need to run the picard command CollectRnaSeqMetrics below

java -jar picard.jar CollectRnaSeqMetrics \
      I=input.bam \
      O=output.RNA_Metrics \
      REF_FLAT=ref_flat.txt \
      STRAND=SECOND_READ_TRANSCRIPTION_STRAND \
      RIBOSOMAL_INTERVALS=ribosomal.interval_list

and I need to create the interval_list for hg38. Is there a list I can download or if I need to create this, could someone kindly advice/guide?

Thanking you in advance!

rna-seq picard qc hg38 interval_list
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updated by sofiahjuler • sofiahjuler • written by hallsalina • hallsalina

2 answers

Here you go:

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written by Dan D Dan D

Hi I also need a intervalist for hg38 for the picard CollectRnaSeqMetrics. Does this list also contain the 5.8S rRNA?

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written by sofiahjuler • sofiahjuler

Just a few days back I was looking answer to the same question and hit upon Kamil Slowikowski's method to generate for hg19. I modified this for GRCh38 and can be found here.

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written by Arindam Ghosh Arindam Ghosh

Thank you @Arindam! I will take a look now.

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written by hallsalina • hallsalina

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