User: inah

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inah • 0
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Posts by inah

<prev • 5 results • page 1 of 1 • next >
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lncRNA annotation for featureCouns and STAR
... Hi,   I have total RNAseq data and one of my main goals is to map lncRNAs (long noncoding RNAs). I am using STAR for alignment and featureCounts for mapping (counting). For the lncRNAs, I think I need to use the annotation file gencode.v28.long_noncoding_RNAs.gtf.gz.  I will pass this annotation fi ...
annotation featurecounts star lncrna written 13 months ago by inah • 0 • updated 13 months ago by Wei Shi • 3.1k
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Comment: C: strange results with featureCounts
... There is still something that must be going wrong with my analysis. I have compared the numbers of protein coding genes present (here meaning present in two samples with counts of at least 5) between mRNA-seq and total RNA-seq data. The mRNA-seg data had library sizes around 24 million, while the to ...
written 14 months ago by inah • 0
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strange results with featureCounts
... Hi,   I have human total RNA-seq data (PE, Next-Seq) from a pilot study with two samples and am getting results from featureCounts that do not make any sense to me. I process the data as follows: (1) I perform adapter trimming using ea-utils mcf and mild quality trimming using btrim. I use STAR for ...
featurecounts rna-seq total rna written 14 months ago by inah • 0 • updated 14 months ago by Gordon Smyth ♦ 38k
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read count summed over exons is greater tham the gene-level read count using featureCounts
... Hi,   I have been using featureCounts to obtain both exon- and gene-level read counts (reads were aligned with STAR). For one particular gene (ARID5B, which has 12 exons, 5 unique to one isoform, 2 unique to another isoform and 5 shared), I find that the read count summed over the 12 exons is greate ...
rsubread featurecounts exon mrnaseq written 2.1 years ago by inah • 0 • updated 2.1 years ago by Wei Shi • 3.1k
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exon counting with featureCounts
... Hi,   I want to obtain read counts at the exon level using featureCounts. I run Rsubread and use these options: annot.ext="/home/inah/RefGTF/GRCh38/annotation/Homo_sapiens.GRCh38.85.gtf", isGTFAnnotationFile=TRUE, GTF.featureType="exon",  GTF.attrType="exon_id",  useMetaFeatures=FALSE The resulti ...
rnaseq written 2.1 years ago by inah • 0

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