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  • Nov 26 13:00
    abshah commented #240
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    manuelsmendoza edited #241
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    manuelsmendoza edited #241
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    manuelsmendoza edited #241
Matt MacManes
@macmanes
if you install the package, you could just use the version of transrate that is included.
tho... I do recommend you use all of the ORP. It has been shown to produce better assemblies that any one standalone assembler (of the ones tested - SPAdes, Shannon, Trinity).
Happy to answer questions about the package, help install, run, etc.
Sandra Victoria Gómez Gutiérrez
@sgomezgu_gitlab
Hi everybody! How are you. Scuse me. I would want to know if you have some solution for this problem. I get this error every time I try run transrate:
Dependencies are missing:
  • blastplus (2.2.[0-9])
    To install all missing dependencies, run:
    transrate --install-deps all
    If you only want the read-metrics dependencies:
    transrate --install-deps read
    Or if you only want the reference-metrics dependencies:
    transrate --install-deps ref
    and when I try to download dependencies I write --install-deps all to install reference module because I want to compare two assamblies. But I get this error:
[ERROR] 2018-07-26 11:26:56 : install-deps all is not valid. You must specify one of: ref.
Muhammad Arslan
@arsilan324_twitter
Hi. I am getting this error. Can someone help?
Unable to download data from https://rubygems.org/ - SSL_connect returned=1 errno=0 state=SSLv2/v3 read server hello A: tlsv1 alert protocol version (https://rubygems.org/latest_specs.4.8.gz)
lmfaber
@lmfaber
Hey everyone,
Since this thread seems to be a little bit more active than the github repository, I'll try my luck here.
I need to use Transrate in my current project (in a conda environment), but i couldn't find a working recipe anywhere.
I managed to create a working conda build (tested and working for me on two different machines). Everyone interested can get and test it from here: https://anaconda.org/lmfaber/transrate
There are currently version 1.0.3 and 1.0.1. If this is working as well for someone else, I would really appreaciate some feedback.
I could further provide the recipes if @blahah is interested?
Cheers
Rik
@blahah
thanks so much @lmfaber !
if you could publish them on github that would be great
and we can link to them if people need them
lmfaber
@lmfaber
@blahah I uploaded the recipes here: https://github.com/lmfaber/transrate_conda Feel free to use them as you need. Would be nice to see them on the bioconda channel sometime. Not the cleanest install, since I'm new to conda. There are many errors during the conda-build process, but however that doesn't affect the functionality. Cheers
Rik
@blahah
thanks very much @lmfaber
PersillaQ
@PersillaQ
Hi @blahah! I installed transrate with lmfaber's conda recipe (thanks!) without any error messages. It seems to work correctly. My analysis gives strange results insofar as I have high mapping rates with both bowtie2 and SNAP (i.e. >90%) but the transtransrate mapping stats are poor with <50% fragments aligned and 100% uncovered transcript. SNAP resports ~40% with a MAPQ>=10, and ~50% with a MAPQ<10. Could this be related (i.e. reads with MAPQ<10 are not counted as aligned?)? Thanks for helping!
Matthew A. Birk
@matthewabirk
@blahah @stuartwillis It looked like transrate v 1.0.4 was on the brink of coming out in April 2017 with the Salmon upgrade (0.4.0 → 0.8.2), but I can't find access to this version. Has this release been made? Are there any plans to release it? Thanks!
matemosaike
@matemosaike
Just wondering if Transrate works with Single-end RNA Seq reads?
Matt MacManes
@macmanes
no it does not
matemosaike
@matemosaike
Do you know any software that does similar analyses for Single-end Reads?
Yogesh Gupta
@bioinfonext_gitlab
I am trying to use Transrate to remove chimeric and low quality contigs from de novo assembly. What should be the cutoff to remove these artifacts from de novo assembly
_fantasticDev_
@SnakeGeneral
Hello everyone!
I want to change a simple asm code to c++ code.
but I am facing problems...
please help me
transparency:
mov eax,00000000
in here transparency is address.
VanesaSGT
@VaneSGT
Hello all,
I'm beginner with this bioinformatic tools and I'm trying to install transrate. The installations seems to be OK, but when I try to run an analysis with the example dataset I get this error:
[ERROR] 2020-04-22 12:10:41 : ReadMetrics: could not find bam-read in path
it happen before with snap but error was solved when I have installed the snap-aligner dependency.
However my problem is that I cannot find a good recipe or channel to install bam-read
Im working on MacOS 10.14
I also tried to load the tar file, but honestly I don't know how to do this manual installation
I will appreciate if someone can help me
VS
Christine Florece
@cmflrc_gitlab
Hi. I am trying to install transrate via conda and it showed me this error:
PackagesNotFoundError: The following packages are not available from current channels:
  • transrate
  • ruby[version='>=2,>=2.6.5,<2.7.0a0']
VanesaSGT
@VaneSGT
you can download the tar file for your system and then keep the path before run the analysis
I have had the same problem. Seems conda only works for linux
VanesaSGT
@VaneSGT
Now I have another problem. I followed the instructions. I extracted the binaries etc.. Now transrate seems to run well but is not. I tested the run with an assembly that I already analyzed in transrate but in our ssh server (transrate works perfectly there). The results for the assembly metrics are good, but the read base metrics are totally different and very bad, means, 98% contigs good for the analysis done in the ssh server, and 15% contigs good with transrate installed in my mac. NO error messages!,
Anybody knows what happen?
Rik
@blahah
@VaneSGT hey, sorry for the issues you've been having. Transrate is quite out of date now, as I've been unable to maintain it for a few years
I saw you posted a github issue - if you can add all your problems there I can at least try to help you run it
VanesaSGT
@VaneSGT
Thanks Rik, I appreciate!
VanesaSGT
@VaneSGT
In future I will post all my problems there ;)
C
@mflc18_twitter
Hi all, I installed all the dependencies needed. However, it says that Salmon is not installed but upon checking on the bin folder of transrate, Salmon is there but as a link. Now, the problem persists every time I run a job.
Joshua Orvis
@jorvis
Same. Does yours error also when you just try to run salmon without arguments?
Abhijeet Shah
@abshah
Hi TransRate users, I too have encountered errors with Salmon (in recent versions of Salmon, the run flags have been changed), and I have managed to fix them. I can post a patch file in the next few days. I hope this can help other TransRate users.
Joshua Orvis
@jorvis
That's great!
Abhijeet Shah
@abshah
Hi TransRate Users, I have finally gotten around uploading my patch to github. I am not sure how well this might work on other systems. Please let me know if you encounter similar errors. I am sure we can figure them out. https://github.com/abshah/transrate
And thanks @jorvis for testing it out first !
Bikash Shrestha
@bshrestha0

I am getting following error while running TransRate,
Dependencies are missing:

  • salmon (0.6.0)
    You are running the packaged version of transrate
    This comes with the read-metrics dependencies pre-installed.

So, I git cloned the patch you have distributed above. I am getting following error while running command $ gem build transrate.gemspec

ERROR: While executing gem ... (Gem::InvalidSpecificationException)
duplicate dependency on bindeps (>= 1.2.1, ~> 1.2, development), (>= 1.2.1, ~> 1.2) use:
add_runtime_dependency 'bindeps', '>= 1.2.1, ~> 1.2', '>= 1.2.1, ~> 1.2'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2608:in block in validate_dependencies' /usr/lib64/ruby/2.1.0/rubygems/specification.rb:2606:ineach'
/usr/lib64/ruby/2.1.0/rubygems/specification.rb:2606:in validate_dependencies' /usr/lib64/ruby/2.1.0/rubygems/specification.rb:2589:invalidate'
/usr/lib64/ruby/2.1.0/rubygems/package.rb:230:in build' /usr/lib64/ruby/2.1.0/rubygems/package.rb:114:inbuild'
/usr/lib64/ruby/2.1.0/rubygems/commands/build_command.rb:48:in execute' /usr/lib64/ruby/2.1.0/rubygems/command.rb:305:ininvoke_with_build_args'
/usr/lib64/ruby/2.1.0/rubygems/command_manager.rb:167:in process_args' /usr/lib64/ruby/2.1.0/rubygems/command_manager.rb:137:inrun'
/usr/lib64/ruby/2.1.0/rubygems/gem_runner.rb:54:in run' /usr/bin/gem:21:in<main>'

And if I try to run tranrate without building it, I get this error:

/usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_require.rb:55:in require': cannot load such file -- transrate (LoadError) from /usr/lib64/ruby/2.1.0/rubygems/core_ext/kernel_require.rb:55:inrequire'
from /work/03125/bikash/phylogenomic/transrate/bin/transrate:2:in `<main>'

Any help/suggestions is greatly appreciated.

Thanks!