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  • May 24 13:27
    VaneSGT opened #238
  • May 24 09:32
    VaneSGT closed #237
  • Apr 26 09:58
    mr-eyes starred blahah/transrate
  • Apr 22 10:20
    VaneSGT opened #237
  • Mar 03 20:04
    blahah commented #216
  • Mar 03 20:02
    dpryan79 commented #216
  • Mar 03 20:00
    blahah commented #216
  • Feb 11 13:17
    gbrsales opened #236
  • Feb 11 12:41
  • Feb 04 01:39
    zjlahey starred blahah/transrate
  • Jan 27 15:42
    upendra2020 opened #235
  • Jan 13 19:54
    rafinhacp commented #232
  • Jan 08 14:12
    sunnykevin19 opened #234
  • Dec 11 2019 15:14
    xz289 starred blahah/transrate
  • Dec 04 2019 13:42
    rafinhacp commented #189
  • Dec 04 2019 02:32
    lychen83 opened #233
  • Nov 30 2019 15:33
    AdamStuckert commented #189
  • Nov 29 2019 23:12
    rafinhacp commented #189
  • Nov 29 2019 23:12
    rafinhacp commented #189
  • Nov 12 2019 09:42
    dpryan79 commented #216
PauloFlores
@PauloFlores
--threads worked fine (linux) with me. Snap is slower than Salmon but 90 million reads shouldnt take very long - couple of hours?
Urwah Nawaz
@urwahnawaz_twitter
Hi all, I've generated a de novo assembly using Trinity and used TransRate to evaluate the accuracy. My transRate score turned out to be very low (0.03). I used other metrics as well (BUSCO, back mapping, ExN50), and so far they all look good. I wanted to know if TransRate would be good for my species (I'm sequencing a cephalopod and they are known to have a highly repetitive content). Any advice on this would be great :)
jereBrand
@Jeremias-Brand
Hi, all. I am running transrate on multiple assemblies simultaneously as part of a large snakemake pipeline. For this I limit threads for each run to a fraction of total cores used. Transrate seems to then only use the global limit. If I run 3 runs with 10 cpus assigned each then all 3 transrate runs will be executed at the same time but only using 10 cores. This is really slowing down the whole pipeline. Any suggestions on how to fix that?=
@blahah
Stuart Willis
@stuartwillis
@blahah is there a 'simple' reason why scores would be different between 1.0.1 (w/ salmon 0.4.2) and 1.0.3 (w/ salmon 0.6.0) for the same assembly? The fragments mapped etc. are much lower for 1.0.3 (e.g. 0.91 vs. 0.29). I tried to swap in the most recent salmon (0.9.?) to see what effect that had but transrate returned 'missing 0.6.0'. Any thoughts?
Rik
@blahah
@stuartwillis sorry for the slow reply. Yes - there's a bug in 1.0.3 - trust the scores from 1.0.1. I'm afraid I've been completely out of action for medical reasons now for going on 10 months. I have along backlog of work to catch up, and am not paid to work on this, but I will get around to releasing a new version with all bugs fixed
in the meantime I suggest following @macmanes procedures for using transrate - he has figured a nice way to include it in a workflow avoiding the pitfalls that have accumulated due to my absence
@macmanes do you have a link to your protocol? I'll add it to the welcome message for this channel
sdbaney
@sdbaney
Does transrate not read fastqsanger files? My downloaded trimmed files from galaxy are downloaded as fastqsanger but every time I try to run transrate with these files, it crashes, and gives me an error. When i run the --assembly with the raw read fastq formatted files, it runs fine. Do I need to somehow convert my trimmed files from fastqsanger to fastq?
Matt MacManes
@macmanes
I usa transrate at the end of the protocol to evaluate the assembly.
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?