Question: How can I create LASTdb for nr.gz data?
0
gravatar for MAPK
2.0 years ago by
MAPK1.5k
MAPK1.5k wrote:

I am trying to do long read alignments for my assembled reads with ncbi protein database. I was trying to use LAST tool available here (http://last.cbrc.jp/doc/last-tutorial.html) using nr.gz database using the command lastdb -cR01 nrdb nr.gz. However, it doesn't seem to work with .gz format. Is there a way I can extract all sequences from nr.gz into fasta format? Or if anyone has better suggestion on what I should be doing to perform this alignment? Thanks for your help in advance.

alignement last • 678 views
ADD COMMENTlink modified 2.0 years ago by h.mon30k • written 2.0 years ago by MAPK1.5k
1

You will need to gunzip nr.gz to get the fasta format file. Based on the tutorial that is what lastdb needs.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax85k

Thanks for the helpful comment.

ADD REPLYlink written 2.0 years ago by MAPK1.5k
2
gravatar for h.mon
2.0 years ago by
h.mon30k
Brazil
h.mon30k wrote:

You can stream with zcat:

zcat nr.gz | lastdb -cR01 nrdb -

You can also stream a compressed fasta file to lastal:

 zcat query.fa.gz | lastal nrdb > query.maf
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by h.mon30k
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