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TRON-Bioinformatics / seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
MIT License
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FPKM instead of RPKM for paired-end data #3

Open marcopretti opened 4 years ago

marcopretti commented 4 years ago

Hi,

I've recently run seq2hla on paired-end data using the following command:

python $seq2HLA -1 $INPUT1 -2 $INPUT2 -r "$OUTDIR/$sample" -p 20

and the expression results produced in the output file were in RPKM. Is the calculation correct?

Best

sebboegel commented 3 years ago

I am not sure, if i understand your question right, but the command looks right to me

marcopretti commented 3 years ago

I mean that for paired-end data the command should output the expression level as FPKM, and for single-end data output as RPKM. That was not the case for paired-end as it was shown as RPKM. Best