Questions tagged [rna-alignment]
The rna-alignment tag has no usage guidance.
29 questions
13
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2
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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....
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9
votes
1
answer
297
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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, ...
- 2,716
8
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1
answer
5k
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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....
- 277
7
votes
1
answer
2k
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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. ...
- 2,716
7
votes
1
answer
105
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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 ...
- 325
6
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3
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136
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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
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2
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5k
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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
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3
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247
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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
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2
answers
2k
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Error creating indices using STAR
I am trying to index wheat genome using STAR through following command
...
4
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1
answer
3k
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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:
<...
- 2,479
3
votes
1
answer
475
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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
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1
answer
2k
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Disk space error while aligning reads using STAR
Hi am trying to align RNA-seq reads using STAR through following commands,
...
3
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1
answer
234
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Assertion `compressBound(0xff00) < 0x10000' failed when using STAR 2.7.9a
This question was also asked on github
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). ...
- 31
3
votes
1
answer
53
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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
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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
2
votes
1
answer
102
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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 ...
- 141
2
votes
1
answer
1k
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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 ...
- 221
2
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0
answers
23
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Extracting RNA reads alignments from a mix of DNA and RNA alignments
I have a fastq file that somehow has a mix of DNA and RNA. It's the sequence data of a DNA sample, but I found one interesting gene that has much higher coverage in exons than in introns. I used STAR ...
- 21
2
votes
1
answer
260
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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 ...
- 79
1
vote
1
answer
257
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 ...
- 13
1
vote
1
answer
506
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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
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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
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1
answer
588
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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:
...
- 2,479
1
vote
0
answers
151
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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
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HISAT2: RNA strandedness
My library is unstranded and the code I'm trying to use is this:
...
0
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1
answer
79
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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
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2
answers
421
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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
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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