Questions tagged [featurecounts]

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How to copy only certain counts for genes in tsv file to new file in linux

Hi there I have generated a counts table of samples I need to compare by differential expression analysis. The layout of the counts table is as follows: Gene_id Sample_A_r1 Sample_A_r2 Sample_B_r1 ...
Justin1609's user avatar
3 votes
1 answer

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
2 votes
1 answer

Connection between Detected Genes and The Read Counts

I have been trying to understand the Seurat for analysing scRNA-seq data. It comes to my mind that the main data is organised in the Seurat object with rows as genes and columns as the cells, and the ...
MK Huda's user avatar
  • 163
1 vote
1 answer

featureCounts segmentation fault on Arch Linux

I am encountering a segmentation fault when attempting to run featureCounts from subread-1.6.3 on even small test data. I installed featureCounts from SourceForge ...
Scott Gigante's user avatar
1 vote
1 answer

What is "unmapped read segments" in the output of samtools idxstats?

samtools idxstats produces a four column output (see here) ...
Roger V.'s user avatar
  • 381
1 vote
5 answers

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp) - almost 100 samples altogether. I have to use the samples data for ...
Praveen's user avatar
  • 11
1 vote
1 answer

Error using htseq-count: Could not retrieve index file

I have a total RNAseq dataset that I aligned using STAR producing BAM files (sorted by coordinates). I am now trying to get counts for the lncRNA sequences using htseq-count, with the command: ...
anjali_yen's user avatar
0 votes
1 answer

Help to understand the code for dipeptide composition calculation (in python)

Dipeptide composition of a protein sequence is the number of times a particular dipeptide (e.g. Arginine-Histidine) occurs in a sequence divided by the total number of dipeptides in the sequence (...
Noob's user avatar
  • 123
0 votes
1 answer

Reads count in metagenomics

Background: I am developing a pipeline for metagenomic studies of human gut microbiote. In particular, I am mapping the reads data originating from shotgun whole genome sequencing onto a gene ...
Roger V.'s user avatar
  • 381
0 votes
1 answer

RNASeq analysis using featureCount and EdgeR

I am using a pipeline (bam -> featurecount-> EdgeR) to do some RNASeq analysis of several groups and sub-groups. For example, I have the following dataset with two types (T1 and T2) and T1 has ...
SBDK8219's user avatar
  • 195
0 votes
1 answer

How do I tell featureCounts to ignore fragments that overlap with more than one feature?

I am using featureCounts from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the ...
Biomagician's user avatar
  • 2,459
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Error generating count data using featurecounts in R

I am doing some RNA analysis and am having issues trying to generate count data. I mapped my reads to a reference genome fasta file (genbank fasta file from ncbi) using bbmap and .sam files as the ...
user14648's user avatar