how to create interval lists for picard?

[sidderb]

Hi,

I need a rRNA interval list file for picard's CollectRnaSeqMetrics, as defined here. Is there a handy tool to create these from a given annotation file or a source of prebuilt files (for ensembl GRCh37)?

[dejavu2010]

co-ask

co-ask the same question

[Jon_Keats]

Fairly easy though not simply explained:

samtools view -H YourBamAlignedToGenome.bam > header.txt
cat header.txt ribosome_locations.txt > GRCh37_ribosome_interval_list.txt

If you need other examples try (http://www.keatslab.org/resources/ngs-tools/ngs-scripts)

[dejavu2010]

jon, thx. I checked your website, really helpful. the question i have now is how to create ribosome_locations.txt? thx

[dejavu2010]

i mean how to create that file for other species, for example, mouse

[Heisman]

You can make the header as described here: http://www.broadinstitute.org/gsa/wi...ference_genome

Then, for your intervals, make lines like:

chr1 1485 4892 + target_1
chr2 3490 9400 + target_2

Everything should be tab-delimited.

[Unicb]

Is "target_1" etc just referring to the gene? i.e. Can I have the same value repeated multiple times for this column, or does each entry have to be unique? target_1 through target_6000?