non-standard fasta header format

Hi there!

I've tried googling my problem, but I really couldn't find any proper answer or meaningful explanations to that.

The vast majority of my sequences in the abyss contig fasta files has the standard header format (e.g. >217 1452 43433)

A few of them show a non standard header looking as the following: >23892451 612 30983 145290-,2958386+,6879596+ or >23914100 434 17555 1186186+,...,8272178+

I would be really grateful if you could help me on this matter and tell me how I should interpret this.

Many thanks in advance!

Matteo

abyss assembly

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updated 10.0 years ago by agata88

• written 10.0 years ago by teone182 •

1 answer

See this: https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#fa

In ADJ format of Abyss files. Seems like the fasta file is connected to adj Abyss file that is why you have extra information in heathers. And it is described in link above.

Hope it helps :)

Best, Agata

• 1 views • link

written 10.0 years ago by agata88

Hi Agata! Thanks for the quick reply and suggestion! I checked the link you posted. It basically says that the other "non-standard" header fields represent sequences IDs overlapping with the subject sequence. So far, so good...it makes sense. However, when I look for the overlapping sequences IDs (in my example let's say 145290) in my whole assembly fasta file, these do not exist….and this is not possible if the "non-standard" fields are related to the adj specifications. Right? Any other thoughts? Maybe Abyss developers know the trick here! ;) Take care Matteo

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written 10.0 years ago by teone182 •