Dear Biostars, Hi
I have 6 sam files (3 for cond1 and 3 for cond2) produced from HISAT2 from mapping Hiseq2000 RNA-seq data to a newly released draft genome.
Now I want to use StringTie and then proceed for DEG analysis but in the StringTie manual it says: "
Every spliced read alignment (i.e. an alignment across at least one junction) in the input SAM file must contain the tag XS to indicate the genomic strand that produced the RNA from which the read was sequenced. Alignments produced by TopHat and HISAT2 (when run with --dta option) already include this tag, but if you use a different read mapper you should check that this XS tag is included for spliced alignments . "
I did not use "--dta" option but when I checked my sam files there is some XS tags in it (e.g: YS:i:0 YT:Z:CP XS:A:- NH:i:1"
Q: So, what must I do? map all reads to reference from beginning, using HISAT2 and --dta option or . . . ?
NOTE: my mapping script for each paired-end reads :
./hisat2 -p 6 -x ht2_base_salmon_genome -1 '/RNA_Seq_Data/C1_clean_left.fq' -2 '/RNA_Seq_Data/C1_clean_right.fq' -S '/RNA_Seq_Data/C1.sam' &> C1.sam.info"