This is a test version of Biostars. For the public version, visit https://www.biostars.org.
The number of axons in a segment

Hi

How I can get how many exons are in a genomes range like below

  > head(df)

  Chromosome    Start   End

          1    64613  5707515
exome genomicsrange r
• 362 views • link
written by zizigolu zizigolu

If it is from human/ a model organism with reference annotation available, then use UCSC Table Browser or Ensembl BioMart to download exon coordinates and then use bedtools to check overlap.

Alternatively, if your query segments are few, you could use the online interfaces (UCSC Table Browser) to provide query segment coordinates and retrieve relevant exons only.

• 0 views • link
written by Amitm Amitm

Hello A!

We believe that this post does not fit the main topic of this site.

Cross-posted and zero effort. Users in multiple communities keep asking you to show effort. At least what you've tried, even if it failed. But you keep ignoring it, I personally find this utterly disrespectful, even though you conststantly keep apologizing for it. I do not buy it. To me this reads like "do my work for me". You are not an inexperienced user who is entering the field. New users might be overwhelmed with new information so it can be difficult to express yourself, difficult to find the right words to put together a good question. That excuse does not hold true for you.

https://bioinformatics.stackexchange.com/questions/12806/calculating-the-number-of-probes-for-a-given-genomic-range

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this