trying to find the read group information for each sample

[SamahElmahdi]

we could not found the samples read group information in the sra database except the library name which is supposed to be as the sample name for example:
Sample: F8_III.3
SAMN07348099 • SRS2376054 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: F8_III.3
Instrument: Illumina HiSeq 2000
Strategy: WXS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED as shown in this website.
https://www.ncbi.nlm.nih.gov/sra/SRX3026983
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5858162
so we supposed that SM=LB=RGID=PU=runID_libraryname , such as SM=LB=RGID=PU SRR5858162_F8_III.3 for one sample and etc..

[SamahElmahdi]

so we supposed to repeat the alignment step as we made it first without the red group information as folow:
cd ~/glaucomaproject/hisat_align
R1="$HOME/glaucomaproject/sample_data/SRR5858162_1.fastq"
R2="$HOME/glaucomaproject/sample_data/SRR5858162_2.fastq"
hisat2 -p 1 -x hisatIndex/Homo_sapiens.GRCh38.dna.chromosome.20 -1 $R1 -2 $R2 -S SRR5858162.sam

[SamahElmahdi]

https://www.biostars.org/p/333353/
this link was helpful for adding read group with hisat2
and the code should be as follow:
hisat2 -p 1 --rg ID:SRR5858162_F8_III.3 --rg SM:SRR5858162_F8_III.3 --rg PL:ILLUMINA --rg LB:SRR5858162_F8_III.3 --rg PU:SRR5858162_F8_III.3 -x $myhisatindex -1 $R1 -2 $R2 -S SRR5858162.sam

[marwaabdelazim]

hisat2 -p 1 --rg ID:SRR5858204_F6_II.1 --rg SM:SRR5858204_F6_II.2 --rg PL:ILLUMINA --rg LB:SRR5858204_F6_II.1 --rg PU:SRR5858204_F6_II.1 -x hisatIndex/Homo_sapiens.GRCh38.dna.chromosome.20 -1 $R1 -2 $R2 -S SRR5858204.sam