I'm Synat, a cancer research student. I'm doing RNAseq experiment looking at differential expression between treatment conditions and looking through pathway analysis too.
I'm doing the alignment using kallisto.. I first built index from fasta file and then mapping it to reference gennome using using index and fastq file as described in kallisto manual. With these two stages, i got abundance.h5 file, abundance.tsv file and fun_info file.
However, as I have been told, this is not the end of alignemnt yet as I got only target ID in the abundance.tsv or abundance.h5. Hence, I need another step, which is gene annotation (assigning gene with specific name) and that may need another gtf file.
In kallisto manual, it has been mentioned briefly about gft file and chromosom file,
However, I am not sure whether that was about gene annotation or serve other purposes.
I got a sample R code from my colleages with folder of each sample containing abundance.tsv, abundance.h5 and run_info and once I run those codes they are all worked and got nice gene annotation/name and finally generated csv file for further analysis. However, once I run those code on my files (abundance.tsv, abundance.h5), gene names were missing.
My question is how could I performed annotation in kallisto using gtf file and generate abundance.tsv, abundance.h5 and run_info files? I am quite new to the field and Hope my question makes sense to everyone in the forum and look forward to hearing from you all.