BED to sequence

[cmccabe]

Is there a tool or code that will extract base sequence from a BED file?
If a amplicon in a BED file covers 100 bases can I obtain that base information?
I believe the coordinates are from ensemble. Thank you.

[alexdobin]

http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html

[cmccabe]

sequeence from BED

Where do I use this command?

getFastaFromBed -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo

bedtools getfasta -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed

I have Bedtools 2.17.0 and have the bed and fasta in the main directory. Thanks.

[GenoMax]

Where do I use this command?

getFastaFromBed -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo

bedtools getfasta -tab -fi NS12911_noonan14.fasta -bed 14noonan.bed

I have Bedtools 2.17.0 and have the bed and fasta in the main directory. Thanks.

Provided Bedtools executables are in your $PATH run the command like this. The output will be stored in the file called "output_fasta.fa" in example below (change name as needed)

getFastaFromBed -fi NS12911_noonan14.fasta -bed 14noonan.bed –fo output_fasta.fa

OR

bedtools getfasta -fi NS12911_noonan14.fasta -bed 14noonan.bed -fo output_fasta.fa

If you need the sequences in Tab format then add -tab.

[cmccabe]

sequence from BED

I do not think I have the executable as I am gettig a bedtools not reconized.
Do you know where I can get the exe.? I have attached a screenshot of the directory and in dos do a cd there first
then use the command:

bedtools getfasta -fi NS12911_noonan14.fasta -bed 14noonan.bed -fo output_fasta.fa - tab

(the directory has the bed and the fasta in it as well but I removed them to decrease the attachment size). Thanks.

[GenoMax]

Oops .. we did not realize that you are referring to windows environment (based on your screenshot).

Descriptions of the bedtools above were for Unix/Linux.

I looked for windows versions and the one I see looked suspect so I am not going to link it here. Official releases of bedtools are only for unix/linux/os x.

Do you have any experience with Unix/command line?

[cmccabe]

sequence from BED

Yes, we have ubuntu 10.0.4 and I think bedtools might be installed on there. Windows would be easier as the files are there, but I will confirm. Thanks

[dnewkirk]

You may be able to use Galaxy as well, which would allow you to keep everything on Windows.

Link: https://main.g2.bx.psu.edu

[GenoMax]

Galaxy may be a good option as suggested by dnewkirk. bedtools should run quickly even on main galaxy.