FragPipe-ready fasta headers and redundancy reduction

[MiguelCos]

FragPipe-ready fasta headers and redundancy reduction

[MiguelCos]

Hello Anthony,

I have been using the combined.spritz.snpeff.protein.withdecoys.fasta.

[acesnik]

Hi @MiguelCos,

Thanks for the message!

Having a lookup table for the variants sounds like a good idea, for sure.

On the redundancy, one thing to be careful about is that Spritz does perform some combinatorics with heterozygous variations. It amends sequences with homozygous variations, and since both the reference and alternate allele could be possible for heterozygous variations, it expands the combinations of those possible peptides. Some of those combinations may be lost if combining all the variants into a single entry.

Anthony

[acesnik]

Are you using combined.spritz.snpeff.protein.fasta or combined.spritz.snpeff.protein.withdecoys.fasta?

[acesnik]

That's great. Thanks for the info!

[MiguelCos]

Hello Anthony @acesnik

I just finished an R script for adapting the combined.spritz.snpeff.protein.withdecoys.fasta in a format convenient to FragPipe.

https://github.com/MiguelCos/spritz_fasta_2_fragpipe_adaptation

The repo contains a small sample fasta and the sample output.

If you check the annotation file, you will see that I didn't give particularly meaningful names to each of the columns because I am not sure how to refer to each piece of info associated with each variant. Is there any way I can get to know better how to interpret those and what are their actual 'names'?

I used the script on two different datasets and in both cases, Philosopher seemed to parse the fasta properly (it didn't crash when using the LFQ pipeline, and the TMT report tables were properly generated using the TMT pipeline). I need to look a little bit closer, but in general, it seems to be working as it should.

Also, many thanks for your clarification regarding the redundancy 'problem'. It then makes sense to keep the variant sequences as they are!

Best wishes,
Miguel