How to calculate TPM from featureCounts output

How to calculate TPM from featureCounts output

0

I would like to find the TPM counts for the GSE102073 study. When i downloaded the raw data from GEO, the raw data are featureCounts output.

First part of the file:

# Program:featureCounts v1.4.3-p1; Command:"/data/NYGC/Software/Subread/subread-1.4.3-p1-Linux-x86_64/bin/featureCounts" "-s" "2" "-a" "/data/NYGC/Resources/ENCODE/Gencode/gencode.v18.annotation.gtf" "-o" "/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/featureCounts/Sample_JB4853_counts.txt" "/data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/STAR_alignment/Sample_JB4853_Aligned.out.WithReadGroup.sorted.bam"
Geneid  Chr     Start   End     Strand  Length  /data/analysis/LevineD/Project_LEV_01204_RNA_2014-01-30/Sample_JB4853/STAR_alignment/Sample_JB4853_Aligned.out.WithReadGroup.sorted.bam
ENSG00000223972.4       chr1;chr1;chr1;chr1     11869;12595;12975;13221 12227;12721;13052;14412 +;+;+;+ 1756    0
ENSG00000227232.4       chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1;chr1        14363;14970;15796;16607;16854;17233;17498;17602;17915;18268;24734;29321;29534   14829;15038;15947;16765;1705

How can i convert this into tpm counts?

I tried the method from this post but it requires a counts file
which i don’t have access to; or this post but i am confused on how to use tximport to get the tpm counts nor the input variable featureLength and meanFragmentLength.

Thank you.


rna


featurecounts


counts


rna-seq


length

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