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BLAT error sequnces

Hello,
I use a BLAT alignment with two files.
But here is the error "Error: sequence name channel_231_read_27_template is repeated in the database, all nemes must be unique"

how to change the sequence header of a Fasta file?

or have you another idea.
Thanks

alignment blat test
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updated by GenoMax GenoMax • written by midox midox

1 answer

If there is only one offending header, edit it directly using an editor of choice otherwise use sed. If the sequences are repeated then take out one of the copies.

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written by GenoMax GenoMax

Is there a possibility of changing the header of sequences ?

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written by midox midox

Something like

$ sed 's/channel_231_read_27_template/channel_231_read_27_template_2/' your_file > new_file

To replace only first instance

$ sed '0,/channel_231_read_27_template/s/channel_231_read_27_template/channel_231_read_27_template_3/' your_file > new_file
• 0 views • link
updated by Ram Ram • written by GenoMax GenoMax

I have three copies.

actually, they are not copies but just the same they header.

How I can change the headers?

$ sed 's/channel_231_read_27_template/channel_231_read_27_template_2/' your_file > new_file

it changes the three headers by "channel_231_read_27_template_2"

another solution?

thanks

• 0 views • link
updated by Ram Ram • written by midox midox 
$ awk 'NR==1,/channel_231_read_27_template/{sub(/channel_231_read_27_template/, "channel_231_read_27_template_2")} 1' your_file
$ awk 'NR==2,/channel_231_read_27_template/{sub(/channel_231_read_27_template/, "channel_231_read_27_template_3")} 1' your_file
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updated by Ram Ram • written by GenoMax GenoMax

there is a lot of repetition.

I want to change the headers of all sequences.

do I change the headers in command line?

Thank you

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updated by Ram Ram • written by midox midox

I am not sure why your fasta headers are repeated in the file.

If the sequences are different then the headers should have been different to begin with. If the sequences are identical then you should be using a non-redundant copy with only one representative of each sequence in your files.

If you still want to proceed you will have to think of a programmatic way to get the headers and then iterate through them to change ones you want.

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written by GenoMax GenoMax

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