Hi everyone,
What I need to do is I need multiple sequence alignment file
I converted the vcf file to consensus fasta and cat all these consensus sequence into multifasta.
In my cat file seq are >1
......>10000
for a.fasta
and >1
......>10000
for b.fasta
when I use clustalw it gives error that sequence have same header THAT MAKES SENSE so what I am planning to do is to convert >1
......>10000
to >1
and >1
......>10000
for b.fasta
to >2
and same for for all my 5 samples
Guide me with command to do that
Please do suggest any help
Regards
So
a.fasta
contains 10000 sequences with headers 1, 2, 3, .... 10000 andb.fasta
contains 10000 sequences with headers 1, 2, 3, .... 10000? You have 5 fasta files like that (a, b, c, d, e) and you want to combine them to a single file keeping their identity, right? It is easy, just change the header in each file and combine them using cat:(If you want to use numbers instead of letters, substitute letters with numbers in the above
sed
commands)Thank you let me try and see whether it answers my problem
Can you suggest me how I can combine
a.fasta
with 10000 sequences having headers 1, 2, 3, .... 10000 .......................into just one header e.gPlease suggest
Concatenate
1. the first line of
a.fasta
and
2. all the lines of
a.fasta
that don't have a ">" with line-breaks deletedThanks let me try this
I understand first part but what does this mean
to remove the new line character
Thank you
I did as directed now I have file with one header e.g
I did this with two files
Now I want to combine them when I did I get
When I want to check both come in one file or not I did
It gives 1. My question is why not 2?
And when I upload this multifasta file on galaxy for multiple alignment it gives badly formatted file error
Please help