How to compare different illumina indices with each other to see how similar or different they are

Question

[Apex92]

Dear all,

I have around two groups of 15 indices of Illumina and I need to compare the two groups with each other and remove the indices that look very similar (differ by one nucleotide) from the two groups. I tried BLASTn and I provide two groups there in the fasta file format but I was not successful to run it. I get this error: Warning: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation.

Is there another way for the thing I want to do?

Thank you in advance.

[jv]

Are you trying to demultiplex a fastqc file? If so, there are tools for that. Else, what do you mean by 'indices'?

Answer 1

[GenoMax]

Using bowtie v.1.3.1

$ more inde
>1
ACAGTGAT
>2
ACTGATAG
>3
ACTTGAGA
>4
AGTCAATA
>5
AGTTCCGG
>6
ATCACGCC
>7
ATGAGCAT
>8
ATGTCAAT
>9
ATTCCTGT
>10
CAAAAGGT
>test1
ATTCATGT
>test2
CAAACGGT

Created a bowtie index with this file, added two test sequences that differ in 1bp and then aligned

$ bowtie -x index -f inde
Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
1       +       1       0       ACAGTGAT        IIIIIIII        0
2       +       2       0       ACTGATAG        IIIIIIII        0
3       +       3       0       ACTTGAGA        IIIIIIII        0
4       +       4       0       AGTCAATA        IIIIIIII        0
5       +       5       0       AGTTCCGG        IIIIIIII        0
6       +       6       0       ATCACGCC        IIIIIIII        0
7       +       7       0       ATGAGCAT        IIIIIIII        0
8       +       8       0       ATGTCAAT        IIIIIIII        0
9       +       9       0       ATTCCTGT        IIIIIIII        0
10      +       10      0       CAAAAGGT        IIIIIIII        0
test1   +       9       0       ATTCATGT        IIIIIIII        0       4:C>A
test2   +       10      0       CAAACGGT        IIIIIIII        0       4:A>C
# reads processed: 12
# reads with at least one alignment: 12 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 12 alignments