Question: converting dexseq_count.py 's output of Gene-exon ID to Transcript Id
0
gravatar for Ice P
2.2 years ago by
Ice P0
United States
Ice P0 wrote:

For my analysis using DEXSEQ, firstly I used following command to generate a GFF file:

dexseq_prepare_annotation.py ../Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf Mus_musculus.NCBIM37.DEXSeq.chr.gff

then i obtained a count file by running

dexseq_count.py

this returned a text output as:

ENSMUSG00000000058:005 30

ENSMUSG00000000058:006 414

ENSMUSG00000000058:007 801

ENSMUSG00000000078:001 450

ENSMUSG00000000078:002 1385

ENSMUSG00000000078:003 645

My question is,

Is there a way I could map these exon files (ENMUSG:001) to their corresponding transcript ID (ENSMUST)?

or

Is it possible to get the output in form of ENSMUSE* instead of ENMUSG:001 etc. Then I can use biomart to map them.

ADD COMMENTlink written 2.2 years ago by Ice P0
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