Question: Export online BLAST+ search to GFF/GTF to use as annotation
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gravatar for joelepaul
6 months ago by
joelepaul0
joelepaul0 wrote:

Hi @ll!

I have now been able to run an online BLAST+ search, and have received some interesting results. Now, I would like to use these results to generate a GFF/GTF file for gene annotation to use in a different pipeline.

However, most guides how to do so seem outdated, as they are only referring to the old blastall software, and not to the online output.

I have downloaded the HitTable as *.csv, but I have no clue as to how to convert it to GTF/GFF format.

The scripts suggested here ( How To Convert Blast Results To Gff ) for instance don't work with the output of the online BLAST+ system. The online BLAST+ system also does not accept output format codes such as "–outfmt 6 " as suggested here: https://mgkit.readthedocs.io/en/0.3.4/scripts/blast2gff.html

Could anyone here help me out?

Thank you!

Joe

annotation • 168 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by joelepaul0

how many genes/sequences do you need to process?

if many, I would suggest to switch to running blasts locally (or at least run blast local with remote option, additional advantage: you will get the use the -outfmt 6 option) . If only a few, do some copy-pasting of the coordinates from the online blast result and create a custom gff from them.

ADD REPLYlink written 6 months ago by lieven.sterck9.5k

Its only about 50 sequences, so I could do it by hand. Now, from the BLAST+ output alone, how would I find out whether it is the forward or reverse string (+, -, .), which is required for the GFF file format?

ADD REPLYlink written 6 months ago by joelepaul0

that you can deduct from the alignment part. If the subject coordinates go from small to large it's forward, if it is large to small it is reverse.

ADD REPLYlink written 6 months ago by lieven.sterck9.5k
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