Incompatibility issue with fasta and GFF (fasta2GFF)

Question

[jaqx008]

Good day to you all, I am about to run a script that requires a fasta and a gff file in the command. But the fatsa and gff I have downloaded from NCBI contain different loci names. for example fasta has the following type loci naming

Bf_V2_22 
Bf_V2_22

Gff has the following type

NW_003101570.1 
NW_003101570.1

I need both of them to have same names. What do I do? would I get the same cordinates in the gff if I convert fasta2gff? ( How do I convert fasta2gff). Or what is a better thing to do ? Thanks

[finswimmer]

Hello jaqx008 ,

where did you download the fasta and gff files exactly?

You cannot convert a fasta file to gff unless the header of the sequence include the necessary information.

fin swimmer

[jaqx008]

Hi finswimmer. I downloaded them from ncbi as mentioned above.

[finswimmer]

NCBI has tones of data. So please be more specific.

Answer 1

[GenoMax]

You probably did not get the sequence from the same location.

$ zgrep ">" GCF_000003815.1_Version_2_genomic.fna.gz
>NW_003101570.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_1, whole genome shotgun sequence
>NW_003101569.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_2, whole genome shotgun sequence
>NW_003101568.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_3, whole genome shotgun sequence
>NW_003101567.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_4, whole genome shotgun sequence
>NW_003101566.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_5, whole genome shotgun sequence
>NW_003101565.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_6, whole genome shotgun sequence
>NW_003101564.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_7, whole genome shotgun sequence
>NW_003101563.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_8, whole genome shotgun sequence
>NW_003101562.1 Branchiostoma floridae genomic scaffold BRAFLscaffold_9, whole genome shotgun sequence

[jaqx008]

Were did you get this from please?

[GenoMax]

I provided a link to the file above.

[jaqx008]

I just found that the same script have to call a x.bed file. my bed file has the loci in the other format which is

Bf_V2_22 
Bf_V2_22

this is probably because the TE.bed was made from the fasta file with Bf_v type naming

[GenoMax]

Then you will either need to remake the bed file or translate those ID's so they match NCBI's identifiers.

[jaqx008]

Do I have to do that manually? and Isnt there a possibility for mismatch of ID?

[GenoMax]

You will need to go back and re-make/process the data to get ID's that match.