So, I'm working with some RNA-seq raw reads, both paired end (2 x 150 bp) and single-end (1x75 bp). These are coming from the same samples, but sequenced differently in 2 rounds. I want to get counts for each at the trasncript level using salmon. For DEseq2 differential expression analysis at the gene level, I just took the raw counts for each sample (sample_1_seq1 and sample_1_seq2 and sum them. This was after checking there was correlation and the 2 experiments were similar. This way, I just got one count for each sample.
With salmon, I got the quant.sf file for each sample. I see inside the length, effectivelength, TPM and NumReads for each transcript. Does anyone have any idea on how could I get one single .sf file kind of "merging" sample_1_seq1 and sample_1_seq2?
Maybe I can provide salmon from the beginning with the 2 sets of reads somehow?
Thank you for your advice