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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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Output consolidation #30

Open garfield39 opened 4 years ago

garfield39 commented 4 years ago

I ran SPALN as multiple jobs and to each job, I gave genome and a chunk of protein as an input. After a successful run, I obtained the GFF3 files for all the individual jobs. Is there a way of consolidating the gene predictions obtained from all these individual files into a single file while processing and filtering the output?

ogotoh commented 4 years ago

I don’t know how to merge existing Gff files, but spaln + sortgrcd can do an equivalent job as follows.

Run several spaln separately with –O12 option: % spaln –Q7 –O12 –d xxx –T yyy A.faa (or A.fna) % spaln –Q7 –O12 –d xxx –T yyy B.faa (or B.fna) … % spaln –Q7 –O12 –d xxx –T yyy Z.faa (or Z.fna)

Then, % sortgrcd –O0 [other options] A.grd B.grd … Z.grd

The output is sorted on the chromosomal location of the predicted genes. Please refer to the document for more details.