Questions tagged [featurecounts]
The featurecounts tag has no usage guidance.
14
questions
0
votes
1
answer
274
views
Featurecount output .txt file from bam file
After running this command:
featureCounts -p -s 2 -a $genome -o $dir"/"$specie"/count_table/"$value".txt" $output_loc -T 8
on the BAM output of ...
- 1,510
0
votes
1
answer
49
views
problem with feature counts of RNA bulk seq paired data- in Rsubread
I did manage to bild index file (from NCBI transcriptome) and perform alingment in Rsubread in R with my fq files. I did get BAM files as a result and no error. However i am having trouble with next ...
- 1,971
3
votes
1
answer
51
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 ...
- 1,510
1
vote
1
answer
4k
views
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:
...
- 5,632
0
votes
0
answers
158
views
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 ...
3
votes
3
answers
84
views
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
...
- 841
0
votes
1
answer
315
views
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 (...
- 752
2
votes
1
answer
54
views
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 ...
- 15k
1
vote
5
answers
933
views
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 ...
CommunityBot
- 1
0
votes
1
answer
690
views
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 ...
- 19.8k
0
votes
1
answer
308
views
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 ...
- 4,212
1
vote
1
answer
2k
views
What is "unmapped read segments" in the output of samtools idxstats?
samtools idxstats produces a four column output (see here)
...
- 19.8k
0
votes
1
answer
507
views
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 ...
- 19.8k
1
vote
1
answer
297
views
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 ...
- 2,173