6
votes
Accepted
How can longest isoforms (per gene) be extracted from a FASTA file?
While the solution from https://bioinformatics.stackexchange.com/users/96/daniel-standage should work (after adjusting for possible python3 incompatibility), the following is a shorter and less memory ...
- 19.8k
5
votes
Accepted
Detect transcript isoform abundance for a specific gene in scRNA-seq
Transcript quantification is a difficult enough problem as it is, when you add the extra difficulty of going from the low read numbers available in scRNAseq if gets even more difficult.
Added to this, ...
- 3,341
4
votes
Detect transcript isoform abundance for a specific gene in scRNA-seq
Looking for alternative splicing in scRNA-seq is difficult, but there is at least one tool that is specifically designed for it:
DISCO. The site does not have too much info, but there is a ...
- 2,209
4
votes
How to identify which isoforms of a gene are actually expressed in my data?
Tools like kallisto or salmon can perform a process call pseudo-alignment that matches reads from RNA-seq data to transcript isoforms present in a reference genome.
You can then look at the output of ...
- 1,394
3
votes
How can longest isoforms (per gene) be extracted from a FASTA file?
Late to the party here, but I like to try to avoid writing scripts when some command line magic will do. It's good practice to index your FASTA so use it.
...
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3
votes
How can longest isoforms (per gene) be extracted from a FASTA file?
Here is a solution in R. Could get really slow with big files. Works for the example you posted.
...
- 1,613
3
votes
Difference between isoforms and paralogs in transcriptoms?
If a reference genome assembly exists, then reference-guided assembly with Trinity will keep paralogs, because it treats each genomic region as a different assembly set.
If a reference genome doesn't ...
- 15.1k
3
votes
How to identify which isoforms of a gene are actually expressed in my data?
If you do as @james-hawley rightly suggests, keep in mind that pseudo-alignment could detect a lot of transcripts with low TPM that are actually false positives, as reported here (it's a paper ...
- 185
2
votes
Accepted
PASA pipeline: compare experimental transcripts to the reference annotation
Answer from the authors:
PASA ends up using gff3 format instead of sam format for uploading the
alignments. If somebody has the gmap gff3 output, then can be done to
just upload that directly ...
- 2,716
2
votes
Accepted
RNAseq alignment: best practices for aligning to multiple isoforms?
The fact that an alignment is unique or not is relative to the genome, not its annotation. In other words, a read will be considered a multimapper (and ignored by some programs) if it can align to ...
- 394
2
votes
Calling isoforms from long read data generated from partially degraded RNA
I haven't used these long-read RNA-seq tools so I could be wrong here. Transcript reconstruction combines reads from the same transcript and should be robust to partial transcripts. In addition, ...
- 6,605
2
votes
Most-abundant isoform identification using 10x scRNASeq 5' short-reads
I don't know how you would define a dominant isoform, to me that is just the most abundant.
Anyway, what you are trying to achieve, I believe, is not possible with ...
- 4,202
1
vote
StringTie discovers less novel isoforms when reference annotation is provided
Not very familiar with what StringTie is doing, but in general reference annotations are helpful in providing a prior for what the tool expects.
I would suggest looking at the manual and using some of ...
- 4,252
1
vote
RNAseq alignment: best practices for aligning to multiple isoforms?
If you want to account for changing abundances of isoforms, use a pseudoaligner like kallisto for counting. And use DEXSeq, not DESeq2, as DESeq2 is intended to be applied to gene counts, not ...
- 2,061
1
vote
Calling isoforms from long read data generated from partially degraded RNA
You could have a go using LAST. I've been developing and using a protocol for mapping cDNA reads that is based around LAST-mapping since 2017. The most recent RY model addition in LAST seems to clean ...
- 15.1k
1
vote
Accepted
Difference between isoforms and paralogs in transcriptoms?
It depends. If you are performing Illumina based RNAseq, which is likely, it is definitely tricky, You should be able to do this in an ideal world because,
a paralogue will contain SNPs, i.e. there ...
M__♦
- 13k
1
vote
Getting sequences of one transcript per gene out of annotation and genome
Here is the custom python script solution:
...
- 5,652
1
vote
Download sequences of isoforms
Col-0 is, to my knowledge, the standard reference Arabidopsis thaliana ecotype, so the easiest way to get the sequences for all genes is to just download them from Ensembl. The nucleotide sequences ...
- 19.8k
1
vote
How can I extract the longest N isoforms per gene from a fasta file?
I know you are asking for a python solution. But maybe you are interested in other ways.
You can use samtools faidx to index your fasta file. The resulting file ...
- 1,352
1
vote
How can longest isoforms (per gene) be extracted from a FASTA file?
This solution is will work for your example and probably all Augustus-derived Fastas, but mileage will vary beyond that.
...
- 5,110
1
vote
How can longest isoforms (per gene) be extracted from a FASTA file?
An ex-coworker (Josep Avril) has written a couple of very useful little scripts that convert fasta to tbl (seqID<TAB>Sequence) and back again. These are ...
- 10.6k
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