Question: making a multi-fasta file out of 9 separate fasta file
1
gravatar for rupashree.choudhury
5 days ago by
rupashree.choudhury10 wrote:

Hi

I want to do a python task which involves extracting the sequence from a multi-fasta file using a file of IDs for Mycosphaerella graminicola genome. I do not have data(multi-fasta file) for this task. Therefore, I downloaded from ENA using the following link. https://www.ebi.ac.uk/ena/data/search?query=Mycosphaerella+graminicola. Now I have 9 separate fasta files containing Mycosphaerella chr 3,chr 4,chr 5, chr 6, chr 10, chr 12, chr 13, chr 15, chr 19,chr 21 whole genome short gun sequencing.

My question 1)how to make a single multi-fasta file using these separate 9 fasta files. 2) Is the multi-fasta file available on web straightway?

Any Help would be highly appreciated! Thanks

sequence • 173 views
ADD COMMENTlink modified 4 days ago • written 5 days ago by rupashree.choudhury10

Thanks genomax cpad0112 for your help

ADD REPLYlink written 5 days ago by rupashree.choudhury10
6
gravatar for h.mon
5 days ago by
h.mon9.6k
Brazil
h.mon9.6k wrote:

1) how to make a single multi-fasta file using these separate 9 fasta files.

cat *.fasta > Mgraminicola.fasta

But why don't you use GCA_000219625.1, it seems the assembly is at chromosome level, with 21 chromosomes.

ADD COMMENTlink written 5 days ago by h.mon9.6k
1

May be better to do cat chr*.fasta > Mgraminicola.fasta.

ADD REPLYlink written 5 days ago by genomax39k

Thanks h.mon for your help

ADD REPLYlink written 5 days ago by rupashree.choudhury10
1

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 5 days ago by WouterDeCoster24k
1
gravatar for cpad0112
5 days ago by
cpad01123.6k
cpad01123.6k wrote:

May be this also works:

$ awk "1" chr*.fa > out.fa
ADD COMMENTlink modified 5 days ago • written 5 days ago by cpad01123.6k
0
gravatar for rupashree.choudhury
4 days ago by
rupashree.choudhury10 wrote:

Thanks genomax and cpad0112 for your help.

ADD COMMENTlink written 4 days ago by rupashree.choudhury10
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