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I use scipy's least_squares in my paleochrono model:
http://github.com/parrenin/paleochrono
I use python as distributed by anaconda.
Specifically, I use the 'trf' method with the tr_solver='lsmr'…
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Hello,
I am trying your script version 2.1 and I am at the step `converting .dat file into searchable .csv`, so `trf` is done.
But it looks like it is extremely slow.
I have almost 5 millio…
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**Is your feature request related to a problem? Please describe.**
Yes. Using the rest API, you provide 3 timestamps: SIP, EXG, TRF. But on a realtime basis using websocket, you provide only SIP time…
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Dear all,
I'm currently integrating TRF in a NextFlow pipeline. Although I've been previously able to use TRF v4.0.9 successfully outside of such framework, it seems I am now facing an issue due to n…
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Hello,
I ran the following command:
miRge3.0 --adapter AACTGTAGGCACCATCAAT --mir-DB miRBase --samples july_fastq_list.txt --libraries-path mirge3_lib/ --organism-name human --tRNA-frag --qiagenumi…
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hi, is there a way to get all predicted target sites per tRF via the web tool? only the first 50K are displayed (targets are shown when searched via genes, as those are less than 50K).
best, kai
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This work is very helpful for my research. I am training detectors using a ViT backbone. I have used RFLA for both a ResNet and a ViT backbone and I find that in either case it improves the detection …
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Hi,
Great tools to explore the tRF comprehensively. May I ask why all the count values are float instead of int? Are they normalized read count? (for example: trna_sample_readcount_matrix.tsv). Tha…
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我输入的命令是trf s.fasta 2 5 7 80 10 50 2000 -l 15
以下是nohup.out的内容
Copyright (C) Dr. Gary Benson 1999-2012. All rights reserved.
Loading sequence...
Allocating Memory...
Initializing data structure…
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I was working on a 19-nt tRF which sequenced as follows:
`GACCGCAUAGCGCAGUGGA`
I tried the built-in Arabidopsis database with the web server and a self-built rice database (IRGSP1.0) on a local m…