You need learn some basic shell commands, like grep.

You need this for this post:

grep -v -f small.txt big.txt > big-small.txt

And what's the most important, try provide enough information when asking problem. Providing some sample data can save you and us a lot of time.

I guess you are continue trying to solve the same problem posted in Fasta file filtering and Remove sequence from fasta file by samtools . Please post several lines of your sequence and ID list files.

One can use 'join' and 'comm'. -v option in join gives incomparable items from the column of choosen file. In example, files are sorted. in general, it is better to join on sorted files.

For eg.

input long_ids.txt:

$ cat long_ids.txt 
a
b
c
d
e
f
g
h

input short_ids.txt:

$ cat short_ids.txt 
a
b
c
d

output:

$ join -v 1  -1 1 -2 1 long_ids.txt short_ids.txt 
e
f
g
h