Single-ended reads are at the end of the forward-reads file so they should not interfere with the ordering of the paired-end files.
Hi all! I am new to transrate and have a question about the conda build. I installed transrate-tools by "conda install -c bioconda transrate-tools" but the only commando that I can execute (and can find in the conda recipes) is bam-read. I am actually looking for the commando to execute transrate to analyse my trinity assembly based on the sequences and reads. Is the conda build incomplete or do I miss something very crucial? Thanks a lot!
you can grab the binary here: http://hibberdlab.com/transrate/installation.html
Are you planning to make a conda build for transrate?
Dear Transrate authors and users, I am using TransRate to evaluate RNA-seq de-novo assembly and surprisingly, I got a very low mapping rate (< 1%). To check the problem, I directly used snap-aligner to map the same dataset and got a high mapping rate (>90%). In another dataset, however, TransRate gave a high mapping rate as well as snap-aligner.
I am confused now and any suggestions or solution will be appreciated.
I am confused now and any suggestions or solution will be appreciated.
Dear transrate authors and users. I am trying to evaluate assemblies generated by transABySS and Oases. The datasets were normalized and then assembled. I checked the transrate score for assemblies generated from various reduction levels of the normalization algorithm. The number of contigs decreased with the decrease in the number of input reads. But surprisingly, the transrate assembly score increased with the decrease in number of contigs. I am a bit confused about it. Shouldnt the transrate decrease with the decrease in the number of contigs. Or am I understanding the algorithm incorrectly. I used the original unreduced dataset for evaluation using transrate
Yes you should be able to do that. It's not a perfect filter but it fits the "quick and dirty" requirement :)
Hi. I recently used transrate to check my transcriptome assemblies derived from Trinity and the assembly scores were incredibly low (around 0.02). I dont know whether I did something wrongly when I run the program or my assemblies are really bad. I once changed my read files manually from .fastqsanger to .fastq since transrate seems doesnt recognize .fastqsanger. Is that a problem?
Hi,
I've installed transrate on my mac to assess the quality of different assemblies. Everything seem to work fine for the contig metrics (2sec for 38K contigs ranging from 200-15000bp). This effectively run either with example data or my own assemblies. However, when I tried to run the read mapping metric analysis (with example data or my assemblies), no (INFO) lines appear below my command line, Additionally Salmon PID seems to run in loop with really memory usage in TOP (99-100% USAGE / 532K memory) and the Global CPU usage is not more than 5% in the activiy monitor. I've tried to move the transrate folder in other locations with no success. Could you please help me on that.
Thanks.
Hi All, I am getting a really low assembly score (0.13) for my seagrass transcriptome. I was wondering how many plant transcriptomes were assessed using TransRate and if we have information on scores from maybe the "model" plants for me to compare my scores to? I know that a score closest to 1 is the best but do we have something that is an ok score? Thanks.
hi @Muskaann, you can see the ORP protocol (https://www.biorxiv.org/content/early/2017/11/22/177253), and corresponding data (https://github.com/macmanes-lab/Oyster_River_Protocol/blob/master/manuscript/orp.csv) for several plant species. In the csv, the
score columns show the scores for the different assemblers, and the opt columns are the optimal scores.
Hi blahah. I performed a mega RNA-Seq assembly (>800 samples, 16 billion of reads, mapped to my plant genome produced near 180,000 contigs) and now I'm trying to filter the results based on Transrate. I'm doing a few tests to understand the resources/running time required (mapping reads to the contigs and inspecting the alignments), and just testing with 10% of the reads apparently I'll need more than 1 week (32 threads) to get the results. "Calculating read diagnostics..." was the last message. Any advice how to increase the speed or how to run transrate with this amount of data?
Hi- I am trying to assess the quality of a reference transcriptome assembly that was assembled with trinity using a sample.tsv file containing paths to replicate (n=5) read files (paired-end). I am hoping to get information about the assembly score with transrate, but am unsure of how to run the read metrics mode (--left --right) with multiple sample files. Is there a way to use this sample.tsv file or list multiple files?
@DeLeoDM_twitter --left=<s> Left reads file(s) in FASTQ format, comma-separated
--right=<s> Right reads file(s) in FASTQ format, comma-separated
--right=<s> Right reads file(s) in FASTQ format, comma-separated
comma-separated should work
@svanscarfo, I think I'm having the same issue. On a Mac Pro, transrate's read mapping analysis doesn't appear to multithread even when I specify multiple threads in the command. Instead, it sits at the salmon stage, using a single thread and taking FOREVER (with no info printout). Did you figure out a solution? Does anyone else have any suggestions? Would love to use transrate but I think it's untenable on a single thread.
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 :)
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
@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?
@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
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?
Hi All, the link to my assembly protocol is here: http://oyster-river-protocol.readthedocs.io/en/latest/. The preprint is here: https://www.biorxiv.org/content/early/2017/11/22/177253. The Gitter channel is here: https://gitter.im/macmanes-lab/Oyster_River_Protocol.
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.