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Questions tagged [rna-alignment]

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2
votes
0answers
34 views

What pitfalls exist with running FastQC on a bam file?

When trying to figure out what was going on with a bad sequencing run of some RNA data, among other usages of FastQC on earlier files in the analysis, I ran it using RNA-STAR-aligned bam files (human ...
3
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1answer
86 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 ...
6
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1answer
647 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....
1
vote
0answers
55 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 ...
4
votes
1answer
110 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 ...
2
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1answer
640 views

Disk space error while aligning reads using STAR

Hi am trying to align RNA-seq reads using STAR through following commands, ...
3
votes
1answer
556 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: ...
3
votes
2answers
590 views

Error creating indices using STAR

I am trying to index wheat genome using STAR through following command ...
0
votes
1answer
125 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: ...
5
votes
1answer
1k 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 ...
5
votes
3answers
114 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 ...
6
votes
1answer
499 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. ...
8
votes
1answer
167 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, ...
6
votes
3answers
114 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 ...
7
votes
1answer
85 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 ...
11
votes
2answers
448 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....