Error when getting rRNA and tRNA rmask table from UCSC

[sindrle]

Im trying to get a GTF with rRNA and tRNA for mm10, as input for --mask-file for Cufflinks.

I chose the rmask table for mm10, filter for "repClass," type rRNA "OR" repClass = "tRNA"

I get this error:

---------------------------------------------------------------------------
Can't start query:
select genoStart,genoEnd,repName,swScore,strand from rmsk where genoName='chr1' and (rmsk.repClass = 'tRNA' OR (rRNA))

---------------------------------------------------------------------------
---------------------------------------------------------------------------
mySQL error 1054: Unknown column 'rRNA' in 'where clause' (profile=<noProfile>, host=mysqlrr, db=mm10)
---------------------------------------------------------------------------


Any help?

[GenoMax]

Alternatively, get the mm10 GTF from Ensembl: ftp://ftp.ensembl.org/pub/release-75...Cm38.75.gtf.gz

Grep out the sections you need

$ cat Mus_musculus.GRCm38.75.gtf | grep "rRNA"

[sindrle]

How would that work if I wanted the whole chrMT instead?

Btw, I use the iGenomes UCSC mm10 GTF, but maybe its the same.

[GenoMax]

How would that work if I wanted the whole chrMT instead?

Btw, I use the iGenomes UCSC mm10 GTF, but maybe its the same.

Try this (should include MT). Any GTF file you wish to use should work. Adjust grep terms as needed.

$ grep -w 'rRNA\|Mt_tRNA\|MT' Mus_musculus.GRCm38.75.gtf > mask_file.gtf

OR

$ egrep -wi 'rRNA|Mt_tRNA|MT' Mus_musculus.GRCm38.75.gtf > mask_file.gtf

[sindrle]

Thank you very much. Oddly I get empty outputs.

When I open mm10 GTF in textedit I cant find chrM. Cant find any rRNA or tRNA as well.

[GenoMax]

At least the Ensembl version of the GTF I linked above has "MT" (not chrM) as the designation. I also see rRNA and Mt_tRNA in that file.

Are you using the GTF from iGenomes site?

[sindrle]

Yes I am using iGenomes.

[GenoMax]

UCSC mm10 GTF from iGenomes appears to be very different than the Ensembl GRCm38 linked above. For one it does not seem to have any chrM annotations. I am getting the Ensembl one from iGenomes and will look at it later today.

[sindrle]

Great! Thank you.

[GenoMax]

Ensembl mm10 GTF file from iGenomes has annotations for rRNA, Mt_tRNA, MT.

[sindrle]

Thanks a lot. Ill try some AWK or grep and see if I can get them out.

[sindrle]

Any chance you know what they are called in the iGenomes UCSC mm10?