cut reads befor N

[Pol8]

Hi,

I have reads with final Ns. Let's say, how can I get from this :

>R1
GGGGGGGTTTTTTTTTTTTTTTNT
>R2
GGGGGGGGGGTTTTTTTTTTNTTNT

to this (basically I want to cut the reads before the first N):

>R1
GGGGGGGTTTTTTTTTTTTTTT
>R2
GGGGGGGGGGTTTTTTTTTT

[dschika]

You could try:

sed 's/^\([ATGC]*\)N\([ATGCN]*\)/\1/g' YOURFILE > NEWFILE

at least if you have a *nix operating system.

[Pol8]

Thanks, that works only for the first hit of my fasta file. How can I do that for all the sequences?

[blancha]

This command is cute and simple.
If there any Ns in the sequence identifiers of your FASTA file, they will also be trimmed off, however.

cut -d N -f 1 test.fa

[[email protected] ~]$ more test.fa 
>R1
GGGGGGGTTTTTTTTTTTTTTTNT
>R2
GGGGGGGGGGTTTTTTTTTTNTTNT
[[email protected] ~]$ cut -d N -f 1 test.fa 
>R1
GGGGGGGTTTTTTTTTTTTTTT
>R2
GGGGGGGGGGTTTTTTTTTT

[GenoMax]

Thanks, that works only for the first hit of my fasta file. How can I do that for all the sequences?

Do you have a dos/OS X formatted file? You may need to pass it through dos2unix/mac2unix utility before using @dschika's code.

@dschika's code works for me.

[dschika]

Is GenoMax's assumption right? That may cause problems...

Just in case:

sed 's/^\([ATGC]*\)N\([ATGCN]*\)/\1/g' test.fa
>R1
GGGGGGGTTTTTTTTTTTTTTT
>R2
GGGGGGGGGGTTTTTTTTTT

... and this solution does not alter the sequence identifiers

[blancha]

I hadn't realised the sed command worked.
@dscika, better than my cut example too.

I'm posting my awk command anyway, since I spent a bit of time researching it.
It will not trim the N in the sequence identifier, like my simpler cut command.

awk -F "N" '{if (NR % 2==0) {print $1} else {print}}' test2.fa

[[email protected] ~]$ more test2.fa 
>R1 N in the sequence identifier.
GGGGGGGTTTTTTTTTTTTTTTNT
>R2
GGGGGGGGGGTTTTTTTTTTNTTNT
[[email protected] ~]$ awk -F "N" '{if (NR % 2==0) {print $1} else {print}}' test2.fa 
>R1 N in the sequence identifier.
GGGGGGGTTTTTTTTTTTTTTT
>R2
GGGGGGGGGGTTTTTTTTTT

[dschika]

Also quite nice!