Transcriptome Generation -Salmon

NDUFB11

Member

Join Date: Jul 2017

Posts: 34
- Share
- Tweet
#1

Transcriptome Generation -Salmon

02-20-2019, 06:39 AM

Hello guys,

I'm analyzing the gene expression profiling in nematode and I want to generate a FASTA file containing the sequence of all the transcripts using Salmon.

It seems that the program can't find a fasta file although I checked and I have in the genome folder named transcripts.fa

It might be that this file contain a sort of error?

Here is the code

Code:

Patrizios-MBP:processing patrizio$ gffread -w genome/transcripts.fa -g genome/ce11.fa annotation/ce11_genes.gtf Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'! Warning: getSpliced(NULL,.. ) called! Warning: couldn't find fasta record for 'I'!

Thank you
Tags: None

Previous template Next

Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications

by SEQadmin2

Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

The systematic characterization of the human proteome has...
- Channel: Articles
Today, 11:48 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM
Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
07-08-2026, 05:17 AM

Topics	Statistics	Last Post
Single-Cell Atlases Skew Toward European Ancestry, Analysis Finds by SEQadmin2 Started by SEQadmin2, Today, 11:10 AM	0 responses 8 views 0 reactions	Last Post by SEQadmin2 Today, 11:10 AM
UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2 Started by SEQadmin2, 07-13-2026, 10:26 AM	0 responses 30 views 0 reactions	Last Post by SEQadmin2 07-13-2026, 10:26 AM
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, 07-09-2026, 10:04 AM	0 responses 39 views 0 reactions	Last Post by SEQadmin2 07-09-2026, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 25 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM

Unconfigured Ad

Transcriptome Generation -Salmon

Latest Articles

ad_right_rmr

News