TPMCalculator
TPMCalculator copied to clipboard
ncbi
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
Hi, I am using TPMCalculator using the following command: TPMCalculator -g file.gtf -d ./ -a -p -e In the current directory, I have sorted bam files deriving from HISAT2 alignment...
Hi! Thanks for developing such a useful tool! :) I've installed it with Bioconda in a linux server and I'm trying to use it to analyze the STAR BAM files...
Hello, I have used TPMCalculator to quantify RNA expression using bam files obtained using HISAT2. For some genes I am getting extremely high intronic TPM counts when compared to exon...
My bam file generated from Star, when I used TPMCalculater, the output files are empty. It complains "Chromosome with name: TraesCS4D01G266700.2 does not exist Chromosome" for all the queries. I...
Hello, thanks for your good tool! My problem is some genes are duplicated in *_genes.out result. I used hisat2 to align reads. ```bash TPMCalculator -g ${GRCh38GTF} -b ${BamDir}/${Sample}.bam \ -c...
New feature to be added
I noticed that if using multiple bam files it generates a table '_data_per_samples.txt' of TPM values for each gene/transcript for each sample. In order to replace FeatureCounts in a workflow,...
Hello, I am not sure I understand the meaning of the -c flag "-c Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the...
I am facing issues with TPMcalculator! First, I noticed that it is counting much less number of genes. Second, among the counted ones there are duplications (same gene_ID in two...
