All Questions
Tagged with rna-alignment rna-seq
15 questions
6
votes
3
answers
136
views
How can I compute gene expression for a set of RNA reads?
I'm trying to compute a gene expression profile for an organism. I have gene nucleotide sequences of the mentioned organism stored in a fasta file and a set of paired reads stored in two separate ...
- 325
6
votes
2
answers
5k
views
5' and 3' bias in Rna-seq data
I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
- 1,272
6
votes
3
answers
247
views
Show presence of known mutation in RNA-seq data
We have RNA-seq fastq data from control (WT) patients and a patient with a point mutation at a known location in one gene.
I'd like to retrieve the reads aligning to that gene and show the presence of ...
- 2,644
5
votes
2
answers
2k
views
Error creating indices using STAR
I am trying to index wheat genome using STAR through following command
...
3
votes
1
answer
475
views
cDNA and alignment mapping
I am confused with RNA seq alignment. My understanding is that after Mature mRNA is isolated from the cell, it is then fragmented and using reverse transcriptase enzyme a cDNA copy is created which is ...
- 31
3
votes
1
answer
53
views
Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol
My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) → trimmomatic (trimmed adaptor sequence, qc report after trimming suggests the ...
- 31
2
votes
2
answers
40
views
Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to ...
- 547
1
vote
1
answer
506
views
Nextflow HISAT2 command exit status 255 with prebuild index
I have a problem with my nextflow pipeline.
My workflow looks like this:
Uncompress the hisat2 genotpye index grch38_genome.tar.gz from https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz
...
1
vote
1
answer
260
views
What is the meaning of split read?
I want to use rna seq data to later perform functional tests on fusion genes.
so before that I need to filter the "best results" (of rnaseq) for deciding which candidates I actually want to ...
1
vote
1
answer
50
views
What is the best way to map/align my reads on a given genome?
I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the ...
1
vote
0
answers
151
views
How to correctly parallelise RSeQC scripts with GNU parallel?
I have a .bam, as ouput from STAR aligner, from which I need to extract some info using RSeQC while using all the computational resources available to increase ...
- 21
0
votes
1
answer
351
views
HISAT2: RNA strandedness
My library is unstranded and the code I'm trying to use is this:
...
0
votes
1
answer
79
views
Is loss/gain of function reflected in RNA-seq transcript counts?
Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification?
- 131
0
votes
2
answers
421
views
Does rRNA depletion protocol give higher number of mapped reads in Intronic regions?
Recently, I have downloaded a publicly available dataset, which are 350 tumor samples. I see the following information from the published paper.
They used Ribo Zero Gold and rRNA was depleted. Strand ...
- 1
0
votes
0
answers
59
views
Best way to align to find inserted sequence
We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is ...
- 95