Hello everyone, I want to count reads from RNAseq using salmon tool, probably because I'm not a bioinformatician (I'm trying hard to be..) but reading the guideline of salmon I'm not able to make it working. I was taught first to create an index which i did it by downloading the transcriptome and generate an index by this command line.
salmon index -t gencode.v29.transcripts.fa.gz -i gencode_v29_idx
Ideally I shoud quantify with gencode_v29_idx as salmon index but in the gencode_v29_idx folder there are banches of files which is not clear to me which file I shuould add to where.. On the manual it says to run this command line
salmon quant -i transcripts_index -l <LIBTYPE> -1 reads1.fq -2 reads2.fq -o˓→transcripts_quant
plus studying on the web I endeded up with this command line, I used the file indexing.log but I don't know if this is correct
(salmon) [@ws7910 RNAseq]$ salmon quant -i /gencode_v29_idx/indexing.log -l --libType A -1 Treated_1_m1.fastq -2 Treated_1_m2.fastq -p 4 --validateMappings -o salm_treated1
It needs to be adjusted but I don't know what
Thank you for help