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.
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survive •
2 answers
For (accurate) TPMs you may want to consider processing your raw sequencing data through Salmon or Kallisto. These programs accurately estimate abundances at the transcript level which results in better TPM estimates. See the bioconductor RNA-seq guide for more info.
If you want to go that route, yes.
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature counts along with the length of your genes/transcripts which can be fetched from reference gtf/gff file.
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This file is your counts file, isn't it?
featureCounts file
Yes, I thought the featureCounts file is your counts file.