User: Colaptes

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Colaptes40
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3 months, 2 weeks ago
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1 year, 1 month ago
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Posts by Colaptes

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Maker2 Transcriptome Input
... Oh, I did not know that! I have been using `altest=` and assuming that it was being used to create hints. Sadly the closest RNA reads are from a fairly distant organism (~35 million years diverged) so I'm not sure `est=` would work well. ...
written 9 months ago by Colaptes40
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Comment: C: Maker2 Transcriptome Input
... Thanks! I will look at guided assembly. Unfortunately many of the species I am assembling do not have a close reference genome yet or I think it is too fragmented for guided assembly. ...
written 9 months ago by Colaptes40
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Maker2 Transcriptome Input
... Hello, I am annotating the genome of a non-model bird using the Maker2 pipeline and I have a question about filtering the RNA input. Since transcriptomes were not available for my species, I downloaded RNA-seq reads from the closest relative on NCBI and built a transcriptome with Trinity. The outp ...
annotation trinity maker2 transcriptome written 9 months ago by Colaptes40
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Comment: C: Building gene trees
... Thank you very much for the advice! That is very helpful. ...
written 9 months ago by Colaptes40
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Answer: A: Need tool for Convert vcf into fa
... Hi, You might want to take a look at VCFx to see if it does what you need: castelli-lab.net/apps/apps_vcfx.php Cheers. ...
written 9 months ago by Colaptes40 • updated 8 months ago by zx87549.3k
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Building gene trees
... Hi, I have low-depth genome sequencing data from several species in a family and I would like to build gene trees as input for analyses with programs like BUCKy and Astral. (I want to estimate a species tree, and assess evidence for introgression between nonsister lineages). I have mapped the reads ...
bucky species tree astral gene tree written 9 months ago by Colaptes40 • updated 9 months ago by Brice Sarver3.5k
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Comment: C: RepBase alternative for maker?
... Thanks! I will try maker with Dfam and the custom library then and see how it goes. ...
written 10 months ago by Colaptes40
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Comment: C: RepBase alternative for maker?
... Is this still the case after they added the new subscription model in April? After making an account I am redirected to a $1395 paywall to download RepBase with an individual academic license. ...
written 10 months ago by Colaptes40
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Comment: C: RepBase alternative for maker?
... As far as I have been able to find a subscription to RepBase now costs $1395 per year as of April for an individual academic license unfortunately. I made an account but when I go to the downloads page for repbase it redirects me to a paywall. ...
written 10 months ago by Colaptes40
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RepBase alternative for maker?
... Hi there, I'm doing a genome annotation of a non-model annotation using Maker and have a question about repeatmasking. My institution does not have a license to use RepBase now that it requires a paid subscription. Is there a good alternative to using RepBase for repeatmasking within Maker? I have ...
genome annotation repbase maker written 11 months ago by Colaptes40 • updated 11 months ago by Charles Warden7.8k

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