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Make a sequence logo from information in a file?

Hi,

I have a text file with results from a screen. I know that "The identifiers in the file are from the hg38 GENCODE V24 basic annotation (table:wgEncodeGencodeBasicV24)"

I then have to make a sequence logo based on the first 15 positions in the transcripts that were found to be significant hits in the screen.

I know that I have to use the website Galaxy and I have found the tool that does this, but my question is how can I "convert" my file so Galaxy recognizes it?

Thanks in advance

galaxy sequence logo pssm ucsc
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updated by Alex Reynolds Alex Reynolds • written by o3964fn4n • o3964fn4n

1 answer

  1. Export your 15 positions to a UCSC BED-formatted text file
  2. Use a script like bed2faidxsta to convert the BED file to a FASTA-formatted file
  3. Use a program like Weblogo to convert the FASTA file to a sequence logo image file or PWM
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written by Alex Reynolds Alex Reynolds

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