All Questions
Tagged with phylogenetics rna-seq
36 questions
2
votes
1
answer
55
views
Salmon Multiple File SCRIPT giving error
Hi I am using Salmon quantitation for multiple fastq paired files using following code
...
- 61
3
votes
2
answers
149
views
Cannot obtain alignment summary after running Bowtie2
I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:
...
2
votes
1
answer
301
views
Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs
I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :(
So I have nearly 200 samples. These are separated into two groups (group I treated with ...
- 237
2
votes
2
answers
72
views
RNAseq alignment: best practices for aligning to multiple isoforms?
I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions.
Many of my (de novo assembled and ...
- 23
2
votes
1
answer
66
views
Is it possible to do homology inference across species using different kinds of NGS data?
Background: I have a list of species that I want to put through homology inference. The goal of homology inference is to investigate the evolution of a trait on a species tree. I want to use the ...
- 217
2
votes
1
answer
84
views
How to make unrooted tree for Likelihood mapping result by using IQ2-tree?
I am a biologist, and I do not fully understand the tree topology of the experimental species.
I used four-taxon set (4 sequences) to identify the Four-cluster Likelihood-Mapping by using
...
- 21
1
vote
1
answer
112
views
How can I get data of single cell RNA sequence with raw count?
I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values.
How can I find the read counts of a dataset?
- 43
2
votes
1
answer
100
views
how to create "sample file" for the qAlign() function after trimming the reads in R
I'm an absolute beginner trying to solve this question "Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments?"
I did trim the ...
- 41
0
votes
1
answer
132
views
How to solve correlation problems between different samples in scRNA-seq?
I am trying to align and merge different samples from NCBI.
I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 ...
1
vote
1
answer
274
views
Why does BWA MEM orientation contradict my library prep method
I have some RNA-seq data from a stranded paired end library prep, with dUTP and UDG preparation, so the orientation should be RF (confirmed with sequencing provider). I assembled the reads with ...
- 347
2
votes
1
answer
440
views
Get Salmon mapping/alignment summary
With HISAT2, after the alignment of fastq files you get an alignment summary like this:
...
- 345
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 ...
2
votes
2
answers
1k
views
Calculate genome coverage and depth from alignment
I have a .bam alignment file and a genome reference .fasta file. I am looking for a easy to use tool (that I can reference in a publication) to calculate the percentage coverage of the reference by ...
- 121
3
votes
2
answers
834
views
Fastq: how can I check if they are from DNA or RNAseq data?
I have (gave me) Illumina fastq files, which I want to use for variant calling, and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report or who to ask.
Many ...
- 131
0
votes
0
answers
27
views
Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt
I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which uses QuasR in the first step.
My list of ...
- 1
1
vote
0
answers
31
views
TCGA dataset: different accession IDs mapped to same location?
I'm currently working on TCGA miRNA dataset. After constructing a reads matrix, I'm trying to find the isoform sequence. In my data, I have the genomic location (isoform_coords). I found that entries ...
- 11
2
votes
4
answers
419
views
What are the applications of DNA or RNA pattern matching? [closed]
I'm assuming we don't do pattern matching in DNA or RNA for the fun of it. So I'd like to know what are the applications of pattern matching or where does it fit in in larger applications?
I'm a ...
- 21
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 ...
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
1
vote
1
answer
2k
views
How to find adapter sequence
I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279)
I want to run cutadapt, but how would I find the adapter sequence so I can run cutadapt?
- 139
1
vote
1
answer
166
views
why in RNA seq don't we only use reference transcriptome?
I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!
- 121
3
votes
1
answer
2k
views
Downloading SRA Files from AWS
I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
- 651
4
votes
2
answers
1k
views
How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
On GISAID they classified the coronavirus using 4 clades(S, G, V, Other).
I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging ...
- 141
1
vote
2
answers
54
views
Download sequences of isoforms
I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any ...
- 11
1
vote
1
answer
317
views
A GTF annotation for GRCH375d version
I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a ...
- 2,232
0
votes
1
answer
18
views
Empty .result in MirDeep Star
I am using MirDeep star tool for RNA sequence alignment. I have tried both GUI version and command line version of this tool. But every time, I am getting empty . result file and .known_mir file. This ...
- 580
3
votes
1
answer
206
views
Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
...
user3962
5
votes
1
answer
219
views
Why is a PacBio read length larger than the aligned reference region?
I recently had some Iso-Seq sequencing done on my organism catfish on the new Sequel platform and got weird alignments for a size selected 4 Kilobase and up fraction after running the isoseq3 pipeline....
- 53
3
votes
1
answer
476
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
5
votes
2
answers
1k
views
Reads mapped to exonic, intronic and intergenic regions
After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason?
...
- 1,272
3
votes
1
answer
963
views
gffread: GFaSeqGet errors on coordinate overhang
Disclaimer: I had this issue posted on Tuxedo Tools users group and shared it on Twitter, but could not get an answer to this from the developers, nor find documentation of this issue online. So, I'll ...
- 2,716
3
votes
1
answer
3k
views
Strange per sequence GC content results
I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination ...
- 631
1
vote
1
answer
584
views
Alignment QC differences between HISAT2 and Qualimap
I used hisat2 for aligning reads to to the genome. I have an alignment summary for sample1 as follows:
...
- 631
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
8
votes
1
answer
2k
views
Interpreting Intergrative Genomic Viewer (IGV)
I was following a tutorial on "Tuxedo Genome Guided Transcriptome Assembly Workshop" and was wondering how to interpret the following:
From what I understand from 'Color Legends', the color blue ...
- 435
10
votes
2
answers
977
views
Building STAR Genome Index for nanopore RNA sequencing
I am aligning a dataset of 1,000,000 reads oh human mRNA sequenced on Oxford Nanopore Technologies' MinION, and would like to use the STAR aligner, using the parameters recommended by Pacific ...
- 2,173