Question: how to merge multi-chromosomes for sacCer3 -- a kind of yeast
0
gravatar for Ashley
11 months ago by
Ashley60
China
Ashley60 wrote:

I have fasta sequence of sacCer3 strain of yeast downloaded form http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/chromosomes/.

Because I need to mapping mu sequence data to this specie, I have to merge them together. Could you tell me how to merge them ( chrI.fa, chrII.fa, chrIII.fa ...) ? May I cat them all together directly by using the script (cat *.fa > all.fa) ?

Any help would be great appreciated.

sequencing rna-seq • 171 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Ashley60
0
gravatar for ATpoint
11 months ago by
ATpoint36k
Germany
ATpoint36k wrote:
find . -maxdepth 1 -name "chr*.fa" | xargs cat > merged.fa

Don't do cat *.fa > merged.fa because it has been reported that sometimes (and I do not know the reasons) the cat command might recognize the output merged.fa and infinitely keeps adding its content to itself.

Also, please use the search function next time as this is a standard task asked many times before ;-)

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint36k

I ve never experienced this infinite loop for cat, but I suppose you can avoid this by using an alternative extension like:

cat *.fa > merged.fasta
ADD REPLYlink modified 11 months ago • written 11 months ago by 2nelly180

Thanks a lot for your help.

ADD REPLYlink written 11 months ago by Ashley60
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