Questions tagged [rna-seq]

Questions should include this tag if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design or transcriptome assembly...

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Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index

I'm trying to run RNA-seq on single-end mouse RNA data (50bp reads) but have very limited RAM (<4 gb) - I don't think I really have a way to work around this memory restriction, and wanted to try ...
mz.'s user avatar
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1 answer
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issue with rna seq analysis

I am working on RNA seq analysis and I would like to know the following things: Current Methods: downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 performed ...
subhiksha sundaram's user avatar
2 votes
1 answer
75 views

Mitochondrial genes - TPM calculation bulk RNA-Seq

This question was also asked on Biostars I was wondering if any of you have encountered a situation for bulk RNA-Seq where, possibly due to low sample quality or presence of dead cells, mitochondrial ...
nick_b55's user avatar
2 votes
0 answers
45 views

How to incorporate negative controls in DESeq2

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any "control" data to set as baseline, either from ...
Karthik Nair's user avatar
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0 answers
50 views

how to use CIBERSORT

I have seen in several articles, the use of CIBERSORT to calculate the proportion of immune system cells using gene expression data, I would like to try it but I have not found how to install it for R,...
María José's user avatar
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1 answer
33 views

HISAT2: RNA strandedness

My library is unstranded and the code I'm trying to use is this: ...
Neophytos Kouphou's user avatar
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0 answers
22 views

Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated

I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
shaimaa Hassan's user avatar
3 votes
0 answers
43 views

how to install cibersort in R, to do deconvolution using my RNA-seq Data with public single cell data

I have RNA-seq Data from lung cancer immunotherapy patients but i don't have any single cell data from my sample, so i wanted to do a deconvolution with a public single cell data. I thought of doing ...
Rita Soares's user avatar
3 votes
1 answer
42 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
3 votes
2 answers
93 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: ...
ALEJANDRA PANDO CACIANO's user avatar
1 vote
0 answers
62 views

Working with Smart-seq3 data, have some questions regarding UMI and bar coding

Most of my experience has been working with genomic data, this time I am working on data from Smart-seq3. RNA excreted by cells in culture medium were processed with Smart-seq3 (From the looks of it, ...
Karthik Nair's user avatar
4 votes
2 answers
81 views

Question about umap using different numbers of pca components as initialization

I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...
Zack's user avatar
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scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?

I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...
Henry Gong's user avatar
0 votes
1 answer
35 views

Paired end reads with different read lengths

I downloaded some raw RNA-seq reads from NCBI using the sra-toolkit (Accession numbers: SRR2053159-64). The reads were generated using ABI SOLiD, and in colour space. I downloaded them in base space ...
Arkajyoti Banerjee's user avatar
-1 votes
1 answer
82 views

Using CSV files continaing scRNA-seq count data from GEO [closed]

I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked a million times before. I am trying to get the single cell expression data of lymph ...
Newbie Bioinformatician's user avatar
1 vote
1 answer
48 views

What are the output files of RNA-Seq from facility?

This question was also asked on Reddit I am new in our lab and I am going to do bulk RNA-Seq. What type of files will we get from the company (Genewiz)? Will it be a bunch of Fastq files? or they give ...
Sina Asadi's user avatar
-1 votes
1 answer
52 views

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions? Regarding code, preferably using Python or R. EDIT: Added a picture of the non-...
SData11's user avatar
3 votes
1 answer
81 views

Applying glmnet to identify predictors for subtypes

I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, your guidance is very much appreciated. So, I have nearly 700 genes with their ...
Angelo's user avatar
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3 votes
1 answer
66 views

Issue with Differential Gene expression analysis with Deseq2

I am using the Deseq2 package to perform a DE analysis on multiple factors. So, basically to perform the analysis I consider patients characterized by the Brugada Syndrome type 1 and other patients ...
Alessia Avon's user avatar
2 votes
1 answer
54 views

DE analysis tool and method for non-coding features

I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as ...
Arkajyoti Banerjee's user avatar
2 votes
0 answers
24 views

Feasible to find genetic variations of two samples using RNAseq data?

I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL. The former expresses a Ptprc-b allele and the latter expresses a ...
geom_na's user avatar
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1 answer
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is it possible to count cell in Violin plot in seurat?

I tried to quantify the number of cells of Fzd9+ Macrophage. how can I know the cell count? thank you
kiseoking's user avatar
1 vote
1 answer
48 views

Filtering criteria for non-coding features with very low counts

I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA counts file that they are abundant in zero counts, and most of the non-zero counts are very low. Now,...
Arkajyoti Banerjee's user avatar
1 vote
1 answer
38 views

Statistical methods suitable for DE analysis of non coding RNAs

I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package. Is the negative binomial method that is ...
Arkajyoti Banerjee's user avatar
1 vote
0 answers
62 views

building custom gtf file with entrez ID for any organism

How do I generate a custom gtf file format for a organism of my interest similar to human gtf file, in the custom gtf file I want to add entrez id to the new custom gtf. My organism is ...
kcm's user avatar
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21 views

Gene Expression Database for Psychological Disorders

Is there a comprehensive database available online of gene expression across the brain taken from individuals with psychological conditions? Resources like the Allen Institute's Human Brain Map (link ...
Lambda's user avatar
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2 votes
1 answer
189 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 ...
Angelo's user avatar
  • 227
0 votes
1 answer
19 views

Looking for datasets of RNA-Seq (or scRNA-Seq) for L1 larvae C. elegans

I was wondering if anyone know of a repository for C. elegans data sets, specifically in L1 larvae stage. Are there any papers or GEO-sets for this organism at this stage? thanks Assa
Assa Yeroslaviz's user avatar
2 votes
2 answers
219 views

Integrate bulk RNA and ATAC-seq genes

I have up and down-regulated genes from bulk RNA result from DeSeq2. Genes that are differential in chromatin accessibility between two conditions from DiffBind. I would like to find the genes overlap ...
Chris's user avatar
  • 101
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1 answer
58 views

What do the numbers mean in these RNA-Seq gene/transcript TPM files?

From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal ...
Macromind101's user avatar
1 vote
1 answer
143 views

Getting VCF file that contain common SNPs from 6 VCF file using isec

I have 6 VCF files, where I would like to obtain the SNPs that are common (by position) in all the 6 files. I have tried this command ...
Mohamed Samir's user avatar
1 vote
2 answers
116 views

How can I delete these lines in my fastq file?

Hi guys =) I'm sorry if this is a repeat but I haven't been able to find an answer using the search field or google. I am trying to edit a fastq file that has a corrupt line. The read in question is ...
Sebastian Quezada's user avatar
1 vote
1 answer
104 views

What statistical test to apply for DE after CibersortX deconvolution?

This question was also asked on Biostars I am running CibersortX in high-resolution mode (which yields estimates of gene values per sample). After that, I want to perform DE between two conditions on ...
Sam's user avatar
  • 279
4 votes
0 answers
48 views

Salmon Pseudo count when dealing with male and female RNA-seq data

I've generated a quant seq data that I intend to use to compare male and female gene expresion, with a focus on sexual chromosome. For my species (three-spined stickleback), it is a classic XY sex ...
Florent Sylvestre's user avatar
1 vote
1 answer
63 views

Gene rank scores from LINCS database: Evangelista et al. 2022

The website https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown can be used to "Identify reversers and mimickers from over 1 million signatures by entering up and down gene sets .. &...
c00kieRaptor's user avatar
1 vote
0 answers
91 views

How to use hashsolo for demultiplexing hashtags?

I am trying to use hashsolo and I want to make sure that I have done things correctly. I did the below: ...
pythonbeginner's user avatar
2 votes
1 answer
150 views

Why is there antisense sequence in RNAseq data

I'm looking at RNAseq data from CCLE. The data is paired-end. Take the cell line Hs578T and the gene HRAS as an example. The cell line carries a G12D mutation (c.35G>A), so the change in cds is: <...
geom_na's user avatar
  • 237
5 votes
2 answers
583 views

Integrating bulk RNA-Seq data with different sequencing depths and from different sources

I am attempting to integrate different bulk RNA-Seq datasets. While this is not ideal, I'm trying to reduce the technical variability in these datasets by using data generated by similar protocols (...
CodingSquirrel's user avatar
1 vote
1 answer
50 views

Test for differences between groups of samples

Sorry if the answer to this should be obvious. I have RNA-expression results from 24 samples which can be divided into 6 groups, (wildtype and two different mutants at two different ages) with a total ...
Sethzard's user avatar
0 votes
0 answers
36 views

How to remove orig ident. already data normalized, scaled assigned cluster/

How to remove orig ident. already data normalized, scaled assigned cluster/ Example, I have 4 sample data. like 1-control, 2- treatment with A, 3- treatment with B, and 4- treatment with C, I want to ...
Sandi's user avatar
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2 votes
2 answers
145 views

How to differentiate DNA fastq and RNA fastq files?

I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I ...
SNanda's user avatar
  • 21
2 votes
2 answers
51 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 ...
DavidR's user avatar
  • 23
0 votes
0 answers
37 views

How would you define a set of active genes from a bulk RNA-seq experiment in one biological sample? [duplicate]

I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest for some downstream analysis. What would the approach be for defining this ...
ricardo3889's user avatar
3 votes
1 answer
429 views

Nextflow Error: failed to read header from "-"

I am trying to run my nextflow pipeline, and have gotten this error: samtools sort: failed to read header from "-" I'm not sure why this error is ...
anne's user avatar
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1 vote
1 answer
53 views

RNAseq: Why would using a more complete scaffold reduce DEGs?

I have a set of RNAseq data for a couple of relatively under-studied species. They're fungi, of the order Hypocreales. The assemblies we're working with are de novo - reference seqs don't actually ...
HKI_PJTB's user avatar
1 vote
0 answers
21 views

Generating gene signature for sample classification and survival analysis patient cohort

This is from this paper The LSC17 score is calculated for each patient as a linear combination of GE of these 17 genes weighted by regression coefficients that were estimated from the training data as ...
PesKchan's user avatar
  • 207
3 votes
1 answer
196 views

Nextflow Pipeline: Unexpected Input "{"

I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in my pipeline. I believe this to be a syntax error, but I am not sure where to correct it....
anne's user avatar
  • 65
1 vote
1 answer
79 views

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
Mary Allen's user avatar
1 vote
1 answer
197 views

Gene symbol list for all protein coding genes in mice

How can I get a csv or a list of the gene symbol names for all the protein coding genes in mice? I have RNA sequencing data and I'm not interested in the non-coding stuff. I'm worried it could mess ...
Angus Campbell's user avatar
2 votes
1 answer
41 views

Inconsistent replicate numbers in RNA-seq

I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake ...
Wang Ming's user avatar
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