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Why counts to tpm gives different values compared to tpm from kallisto?
featurecounts tpm kallisto rna-seq rawcounts written 27 days ago by newbie • 90
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Why there are low assigned reads in featureCounts output and different outputs for quality checks?
reads alignment featurecounts qualimap rna-seq written 7 weeks ago by newbie • 90 • updated 7 weeks ago by rpolicastro • 2.3k
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How does featurecounts deal with the output from Bowtie?
featurecounts rna-seq bowtie written 8 weeks ago by wangdp123 • 250 • updated 8 weeks ago by swbarnes2 ♦ 9.2k
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6 follow
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featurecounts written 7 months ago by chatterjee.arumoy • 10 • updated 9 weeks ago by genomax ♦ 92k
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FeatureCounts (Ensembl based GTF v.s In-built Entrez GTF) variances in count data
bioinformatics featurecounts rna-seq sequencing written 11 weeks ago by harrydolan.dc • 0
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Best normalization method to use with ChIP-seq counts
normalization featurecounts chip-seq counts edger written 12 weeks ago by science_lizard • 0 • updated 12 weeks ago by ATpoint ♦ 41k
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236
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Low Counts with featureCounts
featurecounts rna-seq written 3 months ago by Neat • 0
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170
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Full GTF file vs Subset GTF file
ensembl featurecounts mirna-seq rna-seq written 4 months ago by Arindam Ghosh • 330 • updated 4 months ago by Shalu Jhanwar • 470
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Correlate ChIP-seq to gene expression
chip-seq featurecounts correlation counts rna-seq written 4 months ago by science_lizard • 0 • updated 4 months ago by rohitsatyam102 • 200
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5 follow
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FeatureCounts output does not contain all the genes in the annotation file
rnaseq rice featurecounts bash written 5 months ago by devbt15 • 10
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featureCounts: extremely low rate of 'Successfully assigned alignments'
featurecounts rna-seq written 4 months ago by Yi Chu • 0
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274
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6 follow
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Fixing BAM file errors reported by Picard ValidateSamFile, and in featureCounts' outfile
picard featurecounts validatesamfile bam written 5 months ago by Anand Rao • 330
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197
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featureCounts on antisense genes
featurecounts rna-seq written 5 months ago by till.schwaemmle • 0
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featureCounts strand specify parameter
featurecounts count matrix strand-specify rna-seq written 6 months ago by ek699 • 0 • updated 5 months ago by Biostar ♦♦ 20
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Is Stringtie a suitable tool for both gene and transcript quantification?
gene stringtie featurecounts rna-seq sequencing written 5 months ago by tianshenbio • 70 • updated 5 months ago by i.sudbery ♦ 9.7k
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Read counts at gene and transcript level - hisat2+Featurecounts or Stringtie?+deseq2
stringtie featurecounts deseq2 rna-seq hisat2 written 6 months ago by tianshenbio • 70
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After read mapping, count exons or genes?
genome featurecounts rna-seq written 6 months ago by tianshenbio • 70 • updated 6 months ago by ATpoint ♦ 41k
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Genome with many duplicated genes: allow multimapping in featurecounts?
next-gen featurecounts written 6 months ago by Tatiana • 0 • updated 6 months ago by swbarnes2 ♦ 9.2k
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FeatureCounts results: does it look correct? Why so many unassigned unmapped reads?
featurecounts rna star rna-seq written 7 months ago by tanya_fiskur • 40 • updated 6 months ago by Chyguc • 0
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[Title Edited] How to update the GFF3 wrong file? [was:] featureCounts may be ignore chloroplast sequences in a plant genome when use -t exon and -g ID in a GFF file?
forum featurecounts subread rna-seq written 6 months ago by marcelolaia • 10
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Different length returned by featureCounts and seqtk comp and AGAT
subread agat featurecounts rsubread seqtk written 6 months ago by marcelolaia • 10 • updated 6 months ago by Juke34 • 4.9k
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Reads shown in IGV not quantified by featureCounts
featurecounts rna-seq igv written 7 months ago by a.palmer • 20
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Receiving more reads from exons than whole genes using featurecounts
featurecounts rsubread rna-seq written 7 months ago by till.schwaemmle • 0
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featureCounts: Low % assigned fragments and discrepancy between STAR alignment multi mapped reads
subread next-gen featurecounts star rna-seq written 7 months ago by david.gonzalez • 10
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featureCounts with pseudobam
featurecounts salmon rna-seq pseudobam kallisto written 3.9 years ago by mccormack • 50 • updated 7 months ago by ATpoint ♦ 41k
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How do I decide the mapping quality score in featureCounts?
featurecounts rna-seq quality score written 8 months ago by dark.lord • 30
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featureCounts does not summarise counts from added/reporter genes
subread featurecounts rsubread star rna-seq written 8 months ago by eduardogccm • 10
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Non-overlapping exon set for exon counting (Illumina RNA-seq)
gtf exon subread featurecounts rna-seq written 8 months ago by andreismolnikov00 • 0 • updated 8 months ago by i.sudbery ♦ 9.7k
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featureCount not processing reads
featurecounts rsubread rna-seq written 6.0 years ago by amoltej • 90 • updated 9 months ago by Tom • 530
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9 follow
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How to get read counts on transcript level using featurecounts?
featurecounts geneexpression rna-seq written 9 months ago by newbie • 90 • updated 9 months ago by Gordon Smyth • 2.0k
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