Question: making a multi-fasta file out of 9 separate fasta file
1
gravatar for rupashree.choudhury
9 months 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 • 558 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by rupashree.choudhury10

Thanks genomax cpad0112 for your help

ADD REPLYlink written 9 months ago by rupashree.choudhury10
6
gravatar for h.mon
9 months ago by
h.mon19k
Brazil
h.mon19k 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 9 months ago by h.mon19k
1

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

ADD REPLYlink written 9 months ago by genomax55k

Thanks h.mon for your help

ADD REPLYlink written 9 months 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 9 months ago by WouterDeCoster32k
1
gravatar for cpad0112
9 months ago by
cpad01129.0k
India
cpad01129.0k wrote:

May be this also works:

$ awk "1" chr*.fa > out.fa
ADD COMMENTlink modified 9 months ago • written 9 months ago by cpad01129.0k
0
gravatar for rupashree.choudhury
9 months ago by
rupashree.choudhury10 wrote:

Thanks genomax and cpad0112 for your help.

ADD COMMENTlink written 9 months ago by rupashree.choudhury10
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