Hello everybody
I am new in RNAseq analysis, so I have some trouble trying to study differential gene expression. DEseq manual is really informative to work with but my question is about creating the input file. I found HT count but it needs a gff file and a SAM file with the aligned reads. If there is not a reference genome or transcriptome to download a gff file which is the way to construct it? I suppose by changing a tab delimited file from blastx but which exactly is the format for a gff as an input to HT count? Is there any automated software to annotate the constructed transcripts (output of e.g. Oases or Trinity) and create a gff?
Thanks in advance.
I am new in RNAseq analysis, so I have some trouble trying to study differential gene expression. DEseq manual is really informative to work with but my question is about creating the input file. I found HT count but it needs a gff file and a SAM file with the aligned reads. If there is not a reference genome or transcriptome to download a gff file which is the way to construct it? I suppose by changing a tab delimited file from blastx but which exactly is the format for a gff as an input to HT count? Is there any automated software to annotate the constructed transcripts (output of e.g. Oases or Trinity) and create a gff?
Thanks in advance.
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