Scan Fasta file in Jaspar but says 'longer than 20000 nucleotides'.
Hello!
I am new here.
I just get the fasta sequence from a published BED file using UCSC genome browser.
Now I want to scan a potential transcription factor binding site using Jaspar. However, on the Jaspar website it returns
You are submitting a sequence longer than 20000 nucleotides. This is beyond the scope of the database. Try out ConSite
And the link to 'Consite' is not active
Anyone knows how to work around with this issue? I assume scanning large fasta files converted from ChIP-Seq is a common practice
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Ram
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muhe1985 •
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muhe1985 •
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Usual solution to restrictions at the website is to download and install the software locally.
Thank you!! I am new to bioinformatics, I just googled and did not find that the Jaspar offer desktop version
Try their download link; you should also look at the MEME suite, which can be used with the JASPAR databases.
In cases like this, where part of a service doesn't work, please use the contact options given and inform the people running the service. Running complex services is hard and people really don't always know when they are partly broken.