Thanks for your answer. I want to remove sequences that are in my qual files but are not in my fasta files. I have the list of names of these sequences, and now I want to use it to remove that sequences for the qual files.

An example of my sequences are:

From my fasta file:

>zema223322s001f_A02_.b..abd
aagctcactatagggcgaatggagctcacgcggtggcggccgctctagaa
ctagtggatcccccgggctgcaggaattcgatcgacggacaagtgaacgc
agattcgttccccaacggctacgacgcaaagtaccaaacccaaaatgcag
gcgcgtcggtgcacgggcgcccacgtgggcctgcaccatccgcgccgcac
cgggtctggggcccgcctggactcaacggtcggatctctcgtccctatca
tgcaccgctccgctttcagacagcagttggttctcatcaaagctcgcaac
tacttcctcccctcccttccttcccttccggccgcctcttgtcctcctca
cctcccaaattgaaatcctcctcactccccgcctagggttccgcttcctc
ccccgtccgagcacctcggcggcagcggtggcagcctggaagcagtccca
tctcgtcgccctatacttccctgccgccacacgtctcagtttcttgttcg
gccgctctcctgccggtccgcccatcgcctgaggtaagcgccccgcctgc
agtcgtcctcactactactttttccatcaatctttgccctcgtagtgtgt
gggcctcgtcccctgctagggccctccggggtgaggtccggtagaggcca
cgcgcgaccgcgagcgagcggcctcctgcgaccagggcggagttggcgac
cggtcgatttctcaagctcagcgtagagcgaatgtccagccggtttcaga
tccaaccgcacggtgttttgctactgtaaatgagcgttgattgtttggtc
gatcgattggcctcgcatttcctcaaacctaatttccgggcagaaacatt
tctgaattcctagatagtcccatcttccaacacactgcggaacctagatg
gccaggcaagggtttgtgtggctcgggctggtgcatgtgcccactcctcg
cttctggatgtaagaatgaaggacattggcgctttcagtgcgcgtaagaa
tgtctcatcttgttatgtatgggtatatcacaacgtgggtgtggaatggt
tattatagataactaatgggacatggataggattttggttaggccaattc
catgcgttttaaaatggtgtgggggatattgaattgttnac

from my qual file:

>zema223322s001f_A02q_.b..abd
9 11 15 13 15 17 19 19 19 22 16 25 25 27 14 12 12 9
7 9 8 14 14 16 14 14 8 8 9 15 15 28 25 34 38 41 28
25 23 21 16 16 16 16 16 16 17 18 20 20 20 21 24 24
37 30 25 29 34 36 30 30 23 23 44 34 34 37 50 37 37
37 37 27 29 29 29 27 27 34 34 44 52 52 50 50 59 59
59 59 37 44 44 59 52 52 56 59 59 59 59 38 30 30 38
38 38 59 38 38 38 38 38 38 38 36 36 33 33 43 59 59
50 50 50 59 59 50 38 38 38 45 38 51 50 38 38 50 50
50 50 59 59 59 59 45 33 33 30 33 30 50 50 50 50 50
50 50 59 59 59 59 59 59 59 59 56 51 51 51 56 56 59
59 51 51 51 59 50 50 50 53 53 59 56 53 53 53 56 53
53 53 53 50 50 53 50 53 53 53 53 53 59 59 38 38 38
38 38 59 50 50 50 50 50 50 50 50 50 50 50 50 50 53
50 50 50 59 59 53 53 53 50 50 53 53 53 53 50 50 50
50 50 50 50 50 56 50 50 50 59 50 50 50 50 50 40 50
50 53 53 53 53 50 59 50 50 50 50 53 53 59 59 56 56
51 59 59 59 59 59 53 53 53 53 53 47 47 47 59 50 50
50 44 44 43 59 59 59 59 59 50 50 50 44 53 53 53 53
53 53 44 44 44 44 53 53 53 53 53 53 53 44 44 43 43
41 41 30 29 37 29 36 36 32 32 32 41 35 35 36 36 36
36 29 36 36 32 32 32 34 34 36 43 43 43 43 43 50 50
50 50 50 43 53 43 43 43 43 43 43 41 36 34 34 32 36
43 36 36 38 38 26 27 30 32 36 31 34 27 27 27 27 37
37 43 43 43 43 53 53 53 44 44 44 44 44 44 53 53 44
44 37 34 37 30 41 41 41 41 50 50 50 50 50 50 50 47
41 41 41 38 36 32 24 24 32 47 36 41 41 41 45 50 43
43 43 43 43 43 50 50 53 53 53 44 44 44 43 43 43 47
47 43 50 50 50 50 50 41 41 41 41 32 32 27 32 32 38
36 36 43 47 47 47 47 50 50 50 50 50 50 43 43 43 41
33 37 37 37 37 37 44 44 44 52 52 52 52 52 52 59 53
53 52 59 59 50 50 44 44 44 50 53 53 53 56 56 44 43
59 59 47 47 47 59 59 59 59 59 52 56 52 53 53 52 52
52 52 50 59 59 50 50 50 56 56 56 56 56 52 59 52 52
53 53 53 53 59 59 59 59 52 50 52 52 56 56 59 56 56
56 56 59 56 53 53 53 56 50 47 38 38 38 47 44 44 52
53 53 59 59 59 59 59 59 59 59 59 56 56 59 59 56 50
43 43 37 37 59 59 59 59 59 53 52 52 52 52 52 51 51
50 34 34 37 30 30 30 41 41 41 41 36 30 41 41 41 34
34 34 34 34 41 22 22 16 13 13 18 27 28 32 36 41 41
34 36 24 28 28 28 28 28 45 45 41 47 32 32 26 23 23
26 29 27 34 34 34 37 41 28 28 34 34 34 25 25 19 15
15 21 32 37 41 43 45 41 36 36 36 41 41 43 45 45 45
41 41 41 41 41 50 50 50 50 50 50 45 45 41 41 35 36
33 33 32 32 32 32 32 36 47 25 25 25 24 24 24 33 33
33 28 25 25 23 25 25 38 38 41 28 36 30 30 36 36 41
45 41 37 37 39 39 39 39 50 53 53 53 53 53 51 35 35
35 30 34 44 35 34 34 34 33 33 30 44 44 44 43 50 50
50 50 50 45 41 27 24 24 22 25 25 32 32 37 38 21 23
23 18 21 21 20 18 21 21 18 21 33 33 31 25 25 25 25
28 28 50 45 45 45 45 41 41 38 38 37 37 27 23 22 19
13 8 12 12 21 17 17 21 36 36 43 43 32 32 26 17 17 21
23 30 16 13 13 16 18 15 20 23 30 32 41 34 26 26 17
19 17 15 18 14 21 21 22 23 23 17 14 15 15 13 17 23
23 18 9 9 9 9 9 16 11 11 15 23 23 23 36 26 26 26 32
32 28 23 23 20 14 14 15 15 15 15 13 9 10 10 9 9 14
18 18 25 26 26 36 30 30 36 36 21 23 17 11 11 15 15
13 13 14 15 10 13 13 13 8 6 6 8 11 9 9 10 11 11 18
10 10 11 19 15 17 17 12 13 13 22 24 29 30 15 17 8 8
8 9 9 9 8 8 6 6 7 8 8 6 6 7 9 6 6 6 12 13 15 13 12
9 10 7 7 6 7 8 8 8 9 9 9 9 6 7 8 10 10 7 7 8 8 11 10
12 6 6 7 6 4 5 5 7 13 13 15 13 12 11 11 10 10 6 6 7
6 7 10 8 8 8 8 7 7 7 9 9 9 8 7 7 6 6 7 7 8 11 10 10
10 9 9 7 7 7 6 9 8 9 7 9 7 9 9 8 9 9 9 10 10 11 11
16 22 12 10 7 7 9 10 9 9 11 15 15 13 13 9 7 6 6 7 8
7 9 9 11 7 5 0 5 5

But of course, these are sequences that are in both files. Another problem that I have is that some names of the sequences in the qual file differ a little from the sequences of the fasta. However now I have the list of the names of the sequences that are in the qual file but not in the fasta file and I will like to use them to remove that data form the qual file. Any idea?