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Questions tagged [isoform]

Each of several mRNAs encoded by different transcripts of the same gene. Isoforms can arise by different splicings of the same pre-mRNA. Each isoform gives rise to a different protein sequence.

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StringTie discovers less novel isoforms when reference annotation is provided

I am analyzing PacBio IsoSeq data and I am using StringTie to assemble transcripts. I noticed the difference in the output files when I add a reference genome annotation (-G option in StringTie). In ...
Aleksandra Greshnova's user avatar
2 votes
2 answers

RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions. Many of my (de novo assembled and ...
DavidR's user avatar
  • 23
1 vote
0 answers

Good source for specific Isoforms overexpression in tumor cells (specifically, melanoma)

My group is interested in genetically engineering mice with label for the Slc45a2 gene, since "the protein is expressed in a high percentage of melanoma cell lines". (from Refseq) How can I ...
Tom Gome's user avatar
2 votes
2 answers

Calling isoforms from long read data generated from partially degraded RNA

What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake we processed some samples with poor quality RNA to generate long read. Now we are ...
user3377241's user avatar
2 votes
2 answers

How to identify which isoforms of a gene are actually expressed in my data?

I am new to bioinformatics and have been assigned the task of discovering which isoforms of a certain protein-coding gene are present in the RNA-seq data that I have. There are several isoforms of ...
Sawason's user avatar
  • 21
1 vote
0 answers

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
user977828's user avatar
3 votes
2 answers

Difference between isoforms and paralogs in transcriptoms?

I've assembled RNAseq data into a transcriptoms using Trinity. There's a option to keep only the longest isoforms for each transcripts and it lead me to wonder how it deals with duplicated genes (--&...
LauraR's user avatar
  • 127
0 votes
0 answers

Do I need to study alternative splicing and isoformswitch separately?

I have done a study on isoform switch between different tissue type. Now, many people asking me to study alternative splicing also. But, dont they will give me same results? If there is a significant ...
user3377241's user avatar
1 vote
1 answer

Getting sequences of one transcript per gene out of annotation and genome

I got a genome (data/genome/genome.fasta) and braker-based genome annotation (data/genome/annotation.gff3), now I would like to ...
Kamil S Jaron's user avatar
1 vote
2 answers

Download sequences of isoforms

I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any ...
new_bioinfo's user avatar
2 votes
1 answer

Alternative splicing positions on protein

I have mass-spectrometry data (Human cellsanalyzed and annotated by MaxQuant). I want to find which peptides are covering positions of former splice junctions (on the mRNA sequence), based on protein ...
Itai Roth's user avatar
2 votes
2 answers

How can I extract the longest N isoforms per gene from a fasta file?

The question of how one can extract the longest isoform per gene from a multi-fasta file has been answered expertly in this thread: How can longest isoforms (per gene) be extracted from a FASTA file? ...
Pedro's user avatar
  • 23
3 votes
2 answers

Detect transcript isoform abundance for a specific gene in scRNA-seq

I want to detect the count of isoform transcripts for a specific gene in scRNA-seq data. Data is coming from cells of Mus Musculus. For transcript isoforms I mean the different alternatives provided ...
gc5's user avatar
  • 1,773
6 votes
1 answer

PASA pipeline: compare experimental transcripts to the reference annotation

I would like to ask if anyone has experience in running a subset of the PASA pipeline, in particular for the reconciliation of some experimental 'transcripts' with the reference annotation. In more ...
aechchiki's user avatar
  • 2,656
9 votes
5 answers

How can longest isoforms (per gene) be extracted from a FASTA file?

Is there a convenient way to extract the longest isoforms from a transcriptome fasta file? I had found some scripts on biostars but none are functional and I'm having difficulty getting them to work. ...
ZincFingers's user avatar