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Trinityrnaseq Alternatives
Similar projects and alternatives to trinityrnaseq
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rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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gatk4-genome-processing-pipeline-azure
Workflows used for processing whole genome sequence data + germline variant calling.
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NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better trinityrnaseq alternative or higher similarity.
trinityrnaseq reviews and mentions
Posts with mentions or reviews of trinityrnaseq.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-04-05.
- What are some good examples of well-engineered bioinformatics pipelines?
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Can I get so guidance on how to run sample data in trinityrnaseq-Trinity-v2.13.2 in Ubuntu Linux ?
The screen shot suggests you are not able to actually compile/install trinity. The cmake command is not used to run it. After you download and unpack the trinity software package: https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.13.2/trinityrnaseq-v2.13.2.FULL.tar.gz, you should look at the INSTALL file, which tells you to:
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Beginner question for using dockerized trinity
I'm trying commands from the Docker site and the trinity site. When I try to run the command, it behaves like the code is incomplete (hitting enter just gives me a new line). To my understanding, the issue can be either in the pathway/to/files part of the code, of in the trinityrnaseq/trinityrnaseq part.
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GATK version issue with variant calling following Trinity pipeline python script
For my analysis I am trying to do variant calling on my transcriptome. I am following the Trinity github pipeline for variant calling, in which they provided a python script for GATK for the variant calling. I use SLURM to run this job for me:
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What's your bioinformatics bible? Any bibliography recommendations for experimental design?
Since you're an R user, I would recommend Bioconductor. Here's an excellent tutorial on how to analyze RNA-seq data (make sure that you're R version is up to date!): https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html . However, if you want to assemble raw transcriptome data, then Trinity is a great tool (https://github.com/trinityrnaseq/trinityrnaseq/wiki).
- Can DESeq2 and edgeR be used on Trinity assembled transcripts given that only the longest isoforms are used?
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A note from our sponsor - InfluxDB
www.influxdata.com | 19 Apr 2024
Stats
Basic trinityrnaseq repo stats
6
800
3.3
3 days ago
trinityrnaseq/trinityrnaseq is an open source project licensed under BSD 3-clause "New" or "Revised" License which is an OSI approved license.
The primary programming language of trinityrnaseq is Perl.
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