get_5p_3p_coordsusing the --more-names argument

[yaskermezli]

Hi,

I'm using the get_5p_3p_coords command to extract tss coordinates bed from GRCh38 gif But, using the -n merge_gene_id_name --more-names gene_biotype arguments

That only paste the "gene_biotype" string after each merge_gene_id_name (in all rows)

here an example: chr1 11868 11869 ENSG00000223972|DDX11L1|gene_biotype . + chr1 29569 29570 ENSG00000227232|WASH7P|gene_biotype . -

I don't know if it is the purpose , but form me I was expecting to get some thing like this

chr1 11868 11869 ENSG00000223972|DDX11L1|LncRNA . + chr1 29569 29570 ENSG00000227232|WASH7P|Protein_coding . -

Thank you.

[dputhier]

Hi Yasminia, According to the help section --name is a comma separated list: -n, --names The key(s) that should be used as name. (default: gene_id,transcript_id) So you should try : -n merge_gene_id_name,gene_biotype

--more-names is a comma-separated list of information to be added to the 'name' column of the bed file. It is supposed to be an external name (any text you want to add).

Best

[yaskermezli]

Ah yes ! Thak you

[dputhier]

Hi Yasminia, According to the help section --name is a comma separated list: -n, --names The key(s) that should be used as name. (default: gene_id,transcript_id) So you should try : -n merge_gene_id_name,gene_biotype

--more-names is a comma-separated list of information to be added to the 'name' column of the bed file. It is supposed to be an external name (any text you want to add).

Best

Le mar. 26 avr. 2022 à 14:47, Yasmina Kermezli @.***> a écrit :

Hi,

I'm using the get_5p_3p_coords command to extract tss coordinates bed from GRCh38 gif But, using the -n merge_gene_id_name --more-names gene_biotype arguments

That only paste the "gene_biotype" string after each merge_gene_id_name (in all rows)

here an example: chr1 11868 11869 ENSG00000223972|DDX11L1|gene_biotype . + chr1 29569 29570 ENSG00000227232|WASH7P|gene_biotype . -

I don't know if it is the purpose , but form me I was expecting to get some thing like this

chr1 11868 11869 ENSG00000223972|DDX11L1|LncRNA . + chr1 29569 29570 ENSG00000227232|WASH7P|Protein_coding . -

Thank you.

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