interval_list for hg38

Question

[hallsalina]

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!

Answer 1

[Dan D]

Here you go:

[hallsalina]

Thank you @Dan! Works perfect!

[sofiahjuler]

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

Answer 2

[Arindam Ghosh]

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.

[hallsalina]

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