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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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Almost all spaln mRNA without the final stop codon #48

Closed xiekunwhy closed 3 weeks ago

xiekunwhy commented 2 years ago

Hi,

I found that almost all spaln mRNA without the final stop codon, is there a way to include the final stop codon?

here are my command lines:

makeidx.pl -inp Op-f.gf spaln -t20 -M4 -Q7 -O0 -LS -ya012 -o all_aa.gff3 -d Op-f all.aa

when I use gffread to extract cds sequence from all_aa.gff3, I found that only a few cds sequence with stop codon, only 10/50000.

Best, Kun

ogotoh commented 2 years ago

Dear Kun,

Thank you for your comment. I am preparing a revised version, in which termination codon will be included in outputs of all formats with a protein query. Please wait few days until the next release.

Osamu,

xiekunwhy commented 2 years ago

Wow, I am waiting online.

xiekunwhy commented 2 years ago

Hi Osamu,

Please also update to bioconda when next release is out.

Best wishes, Kun

ogotoh commented 2 years ago

Dear Kun,

I have just uploaded the new version ver.2.4.8. Please confirm that the results are what you want.

I actually don't know how to update bioconda. I will ask someone how to do it.

xiekunwhy commented 2 years ago

Dear Osamu,

The results are exactly what I want, thank you very much.

And I still have some other questions to trouble you. 1) gffread found that some coordinates are wrong (end<start!), not too many, I can ignore these mRNAs, but I think I need to let you know. The following is the log of gffread. all_aa.spaln1.pep.log.txt

2) annotating genomes will be my daily works in next few month, and can you share me the scripts and command lines you have used to generate species-specific parameters, some species I am annotating are mollusc species. I found that you have told someone how to do that (https://github.com/ogotoh/spaln/issues/39), but some part are missing. I may try my best to understand all scripts and command lines if you can share to me.

Best regards, Kun

ogotoh commented 2 years ago

Dear Kun,

Thank you for the examples of wrong coordinates. I will scrutinize the cases to improve spaln’s performance.

I am just developing a scheme by which species-specific parameter sets are obtained more easily than the present scripts do. If the genomic assembly is of high quality and a sufficiently large number of transcript sequences are available, it would not be a hard task. I am trying to get a reliable parameter set when either of the conditions are unsatisfied. Although the final goal would not be reached soon, I will make the developing scripts and additional C++ codes publicly available in a couple of weeks after examination of their integrity.

Osamu,