Comments (10)
Hi Zoe-github2!
Based on your BAM file in the third figure, it seems that the reads were aligned to the transcriptome, and not to the genome. To my knowledge, TPMcalculator works with genome-aligned RNA-seq.
If the input alignments would be from the genome aligned BAM instead of the transcriptome, then it should be able to quantify the expression.
Best wishes,
Lorinc
from tpmcalculator.
from tpmcalculator.
Thanks for the update. I see you used the TranscriptomeSAM option which also generates the transcriptome based BAM file.
Did you run TPMcalculator with the transcriptome or genome aligned BAM? To my understanding, there should be 2 separate BAM files based on your STAR command.
Best wishes,
Lorinc
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Hi Zoe,
A small followup question. Are the missing chromosomes part of the genome fasta file?
If you run a
grep ">" genome.fasta
It should output all fasta entries (where genome.fasta is the path to the fasta file).
Best wishes,
Lorinc
from tpmcalculator.
Hi Zoe,
As Lorinc commented, the BAM file you showed here uses different reference name than your FASTA and GTF, see third column in the BAM file which starts with Tra....
TPMCalculator build a gene model from the GTF using the first column of the GTF as the reference name (chromosome ins this case). Then, the tool assign the reads using the reference name (third column in the BAM file) to the right position on the chromosome.
You need to be sure the BAM files uses as reference the same names that are in the GTF otherwise TPMCalculator won't be able to process the reads.
You can run these commands to see the references on each file:
GTF:
awk '{print $1}' combined.gtf | sort -u
Fasta:
grep "^>" genome.fasta | awk '{print $1}' | cut -c 2-
BAM:
samtools view bamfile.bam | awk '{print $3}' | sort -u
Please, let us know if you need more help.
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Hello,
I think I'm having similar issue.
What exactly the expected output of TPMCalculator is?
Could you specify number out output files and formats?
Or do I have to specify output, like output.txt?
Here's my command, I tried both RefSeq gtf file and UCSC gtf file.
TPMCalculator -g ${hg19genome} -d ${dir}/${Sample} -b ${BAM} -c ${ReadLength}
Regards,
Sumin
from tpmcalculator.
Hello,
I think I'm having similar issue too.
Chromosome with name: xxx does not exist
Here's my command.
TPMCalculator -g xx.gtf -d ${dir/xx.sorted.bam}
Regards,
zhaoshan
from tpmcalculator.
Please, send sample of the GTF and BAM as the original reporter did.
from tpmcalculator.
hello,
I am having the same issue: Chromosome with name: xxx does not exist
here is my sorted.bam file and gtf file
SRR8427257.gtf.zip
I do the following things and check the reference name of gtf file and bam file and they are the same
from tpmcalculator.
Related Issues (20)
- Gene number in input GTF differs from the TPMCalculator output HOT 3
- symbol lookup error HOT 9
- Sets the name of the output HOT 2
- Add a new option to use a directory as output destination HOT 1
- For the paired end reads, is it recommended to use option -p or should i go with default without it? HOT 1
- Output file description HOT 2
- /usr/bin/ld: cannot find -lbamtools HOT 2
- *_genes.out duplicate genes HOT 3
- Compilation error: collect2: error: ld returned 1 exit status HOT 2
- Is the read counting strand-specific? HOT 2
- Key ID for gene name was not found on GTF line HOT 3
- No TPM values, no reads processed HOT 9
- Chromosome with name: ENST.... does not exist HOT 10
- Output files desctiption HOT 1
- Installation without docker HOT 1
- Meaning of "UniqueReads" in genes.out file? HOT 2
- Possible to use gff3 in TPMCalculator v 0.4? HOT 1
- Build problems on Ubuntu and MacOSX HOT 1
- Help me please HOT 1
- After installing version 0.0.4, -version still prints 0.0.3
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