ncbi / TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

ncbi/TPMCalculator Issues

Add a new option to use a directory as output destination
Updated 5 months ago1
After installing version 0.0.4, -version still prints 0.0.3
Updated 5 months ago
TPMCalculater, the output files are empty
Updated 6 months ago10
Possible to use gff3 in TPMCalculator v 0.4?
Updated 6 months ago1
Help me please
Updated 6 months ago1
Meaning of "UniqueReads" in genes.out file?
Updated 6 months ago2
Output files desctiption
Updated 6 months ago1
No TPM values, no reads processed
Updated 6 months ago9
Build problems on Ubuntu and MacOSX
Updated 6 months ago1
Key ID for gene name was not found on GTF line
Closed 2 years ago3
Installation without docker
Closed 2 years ago1
Chromosome with name: ENST.... does not exist
Closed 2 years ago10
For the paired end reads, is it recommended to use option -p or should i go with default without it?
Closed 2 years ago1
/usr/bin/ld: cannot find -lbamtools
Closed 2 years ago2
Input files and GeneID Errors
Updated 2 years ago5
Compilation error: collect2: error: ld returned 1 exit status
Closed 3 years ago2
Is the read counting strand-specific?
Updated 3 years ago2
*_genes.out duplicate genes
Updated 3 years ago3
symbol lookup error
Closed 3 years ago9
Output file description
Closed 3 years ago2
Installation api/BamReader.h: No such file or directory
Closed 6 years ago5
ID with "#" in _genes.out file
Closed 6 years ago7
Gene number in input GTF differs from the TPMCalculator output
Closed 3 years ago3
Different results based on seq. depth
Closed 3 years ago4
Sets the name of the output
Closed 3 years ago2
Output read counts file?
Updated 3 years ago
how to generate the Output file: [genes|transcripts]_data_per_samples.txt ?
Closed 4 years ago12
Question about the -c fag and multi-mappers
Updated 4 years ago3
Chromosome with name: A01 does not exist
Closed 4 years ago4
TMPcalculator mising genes and duplicating other genes
Updated 4 years ago3
Multimapped Reads
Updated 4 years ago1
unrecoginized command line option std=c++14 on compilation
Closed 4 years ago1
Pool BAM file and get TPM for each BAM experiment ?
Closed 4 years ago3
libbamtools.so.2.4.0: cannot open shared object file: No such file or directory
Closed 4 years ago4
77660 Segmentation fault
Closed 4 years ago9
GTF error: "Key for isoform name was not found on GTF line"
Closed 4 years ago4
Nothing in the output files.
Closed 5 years ago18
Compatibility with NCBI GFF3 genome annotation
Updated 4 years ago
Add multithreads
Updated 4 years ago
Add the gene strand to the overlap model.
Updated 4 years ago
Add the read strand to the count model
Updated 4 years ago
CPM output
Updated 4 years ago1
Adding +1 to exon end.
Updated 4 years ago1
Question on TPMCalculator : bam pre-treatment needed ?
Closed 5 years ago3
Raw counts from paired-end alignments seem to be inflated by a factor of 2
Closed 5 years ago6
Compatibility with gencode GTF
Closed 6 years ago2
A critical issue: different number of genes in output for different BAM files
Closed 6 years ago3
Threads
Closed 5 years ago2
TPMCalculator is not working with the Ensembl genome annotation
Closed 6 years ago1
Is it possible to provide a binary version of TPMCalculator
Closed 6 years ago7