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Immortal2333 / Telomeres_and_Centromeres

This is a method to find telomeres and centromeres in plants.
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The meaning of Fig. 3C in the paper #5

Closed MuyuenHoshino closed 1 year ago

MuyuenHoshino commented 1 year ago

Dear Immortal2333, I'm really sorry I keep raising issues, but it should be over soon. Could you please provide some details about this Fig,like what does it mean, what data is used to draw it, etc. image Best wishes

MuyuenHoshino commented 1 year ago

So it is the clustering of the centromere sequence?Can the centromere sequence file be obtained through this pipeline?

Immortal2333 commented 1 year ago

So sorry to reply late.

This is the clustering of the centromere sequence. The cons_seq=XXX sequence of the longest 107-bp is extracted from each chromosome in the genome_trf.split.txt file. You can sort it in ascending order based on the number of copies of period=107. After reverse complementarity of the repeat unit of consensus sequence (if necessary) and setting a starting position, you can align and visualize it using DNAman or GeneDoc software. Just like the figure depicted in this paper.

Best regards

MuyuenHoshino commented 1 year ago

Dear Immortal2333,

Thank you very much for your timely and useful reply. I am an undergraduate student majoring in computer science and have almost no biological foundation. With your help, I have completed the entire pipeline. Thank you again.I wish you all the best in your research endeavors

Best regards