Seqkit concat removing few species
0
0
Entering edit mode
2.1 years ago
lokdeep17 • 0

I am using seqkit concat to concatenate few multifasta files. When I concatenated and looked at the final output, I realized one species is missing. No matter how many times I try it, the species is always missing from the output file. I checked in the input files, the species is present. Moreover, this species is not the least occurring species. For example, I have total 105 files, the species which appeared least is 87 times ( but this species is there in the concatenated file output also), while the species which keep on missing from output occurred 97 times in the input files. Please give some suggestions.

gene seqkit fasta sequence concat • 653 views
ADD COMMENT
0
Entering edit mode

What is the exact command you're using?

ADD REPLY
0
Entering edit mode

Also, please provide an example of the files, especially the problematic region.

ADD REPLY
0
Entering edit mode

Hello Friends, I solved it with some trial and error. For future enthusiasts, it turns out, if your initial files are having unequal number of species than the output files will have less number of species, but if you have equal number of species to begin with, then the output file will have same number of species. For example, if you have 30 multifasta files that you want to concatenate using seqkit concat and you are studying the effect on 25 species. All files have different number of species depending on the gene gain/loss pattern in the species. Now, if your initial two files to be concatenated have 25 species (i.e. for these genes no species show gene loss), then your output file will also have 25 species, but let's say if your one initial file was having 23 species and one was having 25 species then the output file will have only 23 species and all the trailing files will also end up having 23 species only.

ADD REPLY
0
Entering edit mode

Thanks for following up but without code and data examples it is hard to reproduce any of what you say. Keep that in mind for future questions :)

ADD REPLY

Login before adding your answer.

Traffic: 1026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6