Question: getting sequence for a list of miRNAs
1
gravatar for A
4.3 years ago by
A3.9k
A3.9k wrote:

hi,

I have a list of miRNAs IDs from different organisms how I can take sequence of mature miRNAs for all my IDs?

for example

lgi-mir-34

mdo-mir-193

mdo-mir-21

mdo-mir-302d

mml-mir-18

mirnas • 1.1k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by A3.9k
3
gravatar for GenoMax
4.3 years ago by
GenoMax95k
United States
GenoMax95k wrote:

From miRBase using this file.

ADD COMMENTlink written 4.3 years ago by GenoMax95k

thank you, but this is whole of IDs, for example if I want only 100 IDs from which what should I do?

ADD REPLYlink written 4.3 years ago by A3.9k
1

grep -A 1 your_ID them out of the miRBase file using a loop OR use filterbyname.sh from BBMap OR use samtools faidx as described here: A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by GenoMax95k
1

I think grep -A 1 -F -f filewithids.txt mirbase.fa would also do the trick and avoid looping.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by WouterDeCoster45k

thank you both friends

ADD REPLYlink written 4.3 years ago by A3.9k
2
gravatar for A
4.3 years ago by
A3.9k
A3.9k wrote:

another way was mirdeep2

fastaselect.pl reads.fa reads_select.ids > reads_select.fa

This script only prints out the fasta entries that match an id in the id file.

ADD COMMENTlink written 4.3 years ago by A3.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1113 users visited in the last hour
_