Questions tagged [rna-alignment]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0 votes
0 answers
18 views

Assertion `compressBound(0xff00) < 0x10000' failed when using STAR 2.7.9a

I am using STAR 2.7.9a. In the last two days, I am getting an error when running alignments with STAR (independently from the data and genome index I am using). What could be causing this error, which ...
RobAlbn's user avatar
0 votes
1 answer
76 views

HISAT2: RNA strandedness

My library is unstranded and the code I'm trying to use is this: ...
Neophytos Kouphou's user avatar
3 votes
1 answer
43 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 ...
xtian's user avatar
  • 31
1 vote
1 answer
130 views

Only the first file Pair is processed from Channel.fromFilePairs()

This is my first nextflow pipeline and i am struggling with the .fromFilePairs concept of Nextflow. I want to process paired-end read files and align them against a reference genome. I use Hisat2 so ...
stfn.snk's user avatar
0 votes
1 answer
59 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?
Kermit's user avatar
  • 131
0 votes
1 answer
420 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 ...
Thomas Müller's user avatar
1 vote
1 answer
201 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 ...
beachwildernessgene's user avatar
2 votes
1 answer
85 views

Understanding ViennaRNA RNAdistance scoring table

I'm trying to compare the output of 2 different algorithms of RNA structure prediction (my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA ...
Eli Zatlawy's user avatar
0 votes
1 answer
45 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 ...
Dmitrii Trubetskoy's user avatar
0 votes
0 answers
49 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 ...
Sethzard's user avatar
0 votes
2 answers
347 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 ...
maven's user avatar
  • 1
2 votes
2 answers
39 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 ...
Charles's user avatar
  • 537
2 votes
1 answer
1k views

What pitfalls exist with running FastQC on a bam file?

I was analysing a bad sequencing run of some RNA data using FastQC, I supplied it RNA-STAR-aligned bam files (and the human reference). The output of MultiQC had many more "unique reads" in ...
hepcat72's user avatar
  • 221
3 votes
1 answer
424 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 ...
drpreeti3628's user avatar
8 votes
1 answer
4k views

What are "split reads" and "intron clusters?"

I'm working through the example data set for LeafCutter and the documentation mentions "split reads": This will cluster together the introns fond [sic] in the junc files listed in test_juncfiles....
CelineDion's user avatar
1 vote
0 answers
143 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 ...
Tain Luquez's user avatar
2 votes
1 answer
249 views

Merging ssu-align alignments

ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models: archaeal, bacterial eukaryotic Approach Given a set of archaeal and ...
Eli Korvigo's user avatar
3 votes
1 answer
2k views

Disk space error while aligning reads using STAR

Hi am trying to align RNA-seq reads using STAR through following commands, ...
Ammar Sabir Cheema's user avatar
4 votes
1 answer
3k views

Can I run STAR without an annotation file?

I wish to use Rascaf to scaffold a fragmented draft genome. For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome. So, I indexed the draft genome with STAR like this: <...
Biomagician's user avatar
  • 2,459
5 votes
2 answers
2k views

Error creating indices using STAR

I am trying to index wheat genome using STAR through following command ...
Ammar Sabir Cheema's user avatar
1 vote
1 answer
526 views

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

I am running the following command to index my genome: ...
Biomagician's user avatar
  • 2,459
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 ...
stack_learner's user avatar
6 votes
3 answers
230 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 ...
Peter's user avatar
  • 2,634
7 votes
1 answer
2k views

STAR-long parameters for aligning RNA ONT reads to genome

Are there any suggested parameters to align ONT reads to the reference genome using STAR-long? For now, I used the parameters suggested here, but I noticed a weird behaviour. I have RNA reads (D. ...
aechchiki's user avatar
  • 2,676
8 votes
1 answer
282 views

Convert local alignments to spliced alignments in SAM file

I mapped RNA reads to reference genome, using LAST in split mode, and converted the MAF alignment to SAM with maf-convert. My problem is that the transcripts are not reported in a spliced manner, ...
aechchiki's user avatar
  • 2,676
6 votes
3 answers
130 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 ...
hhoomn's user avatar
  • 325
7 votes
1 answer
103 views

How to interpret contig-alignment.psa produced by velvet

I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using ...
hhoomn's user avatar
  • 325
13 votes
2 answers
502 views

What to use to edit RNA alignments?

I have many alignments from Rfam Database, and I would like to edit them. I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ? e....
Peter's user avatar
  • 353