Question: MAGMA Annotation error
0
gravatar for naomibreslin95
2.1 years ago by
naomibreslin950 wrote:

I am trying to run the annotation for MAGMA using the Gene locations, build 37 and european populations.

When I run the following code:

magma --annotate window=20,20 --snp-loc NCBI37.3.gene.loc --gene-loc g1000_eur.bim --out build

It skips every line and gives the error:

WARNING: on line 5522658, chromosome code 'rs188565905' not recognised; skipping gene (ID = 4)

at every position.

Also only a log file is produced. All of my files are in the same directory and they were taken from the magma site. Any information on where the issue lies?

error magma annotation • 747 views
ADD COMMENTlink modified 2.1 years ago by h.mon30k • written 2.1 years ago by naomibreslin950

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 2.1 years ago by RamRS27k
0
gravatar for h.mon
2.1 years ago by
h.mon30k
Brazil
h.mon30k wrote:

I have never run MAGMA, but just by reading you command-line, it appears to me you are swapping the arguments:

--snp-loc NCBI37.3.gene.loc

--gene-loc g1000_eur.bim

Shouldn't be the other way around?

--snp-loc g1000_eur.bim --gene-loc NCBI37.3.gene.loc

The error message indicates the same:

hromosome code 'rs188565905' not recognised

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by h.mon30k
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