Question: interval_list for hg38
1
gravatar for hallsalina
11 months ago by
hallsalina20
hallsalina20 wrote:

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!

ADD COMMENTlink modified 11 months ago by Arindam Ghosh300 • written 11 months ago by hallsalina20
1
gravatar for Dan D
11 months ago by
Dan D7.1k
Tennessee
Dan D7.1k wrote:

Here you go:

ADD COMMENTlink written 11 months ago by Dan D7.1k

Thank you @Dan! Works perfect!

ADD REPLYlink written 11 months ago by hallsalina20
0
gravatar for Arindam Ghosh
11 months ago by
Arindam Ghosh300
India
Arindam Ghosh300 wrote:

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.

ADD COMMENTlink written 11 months ago by Arindam Ghosh300
1

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

ADD REPLYlink written 11 months ago by hallsalina20
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