Hi All this is my first time posting and asking a question so bear with me. I am attempting to use HiSat2 and StringTie for to do some DGE analysis.
Here is my code so far for one sample:
module load HISAT2/2.2.1-foss-2019b
1)Create HISAT2 index for S. invicta genome
extract_splice_sites.py $chandra1/UNIL_Sinv_3.0/chr16.SB.NCBI_v3.4.gtf >$chandra/SinV.ss extract_exons.py $chandra1/UNIL_Sinv_3.0/chr16.SB.NCBI_v3.4.gtf >$chandra/SinV.exon
hisat2-build --ss $chandra/SinV.ss --exon $chandra/SinV.exon $chandra1/UNIL_Sinv_3.0/GCF_016802725.1_UNIL_Sinv_3.0_genomic_1.fa $chandra/SinV_tran
2)Map Reads for each worker brain sample to the reference genome
hisat2 -p 8 --dta -x $chandra/SinV_tran $chandra1/worker_brains/SRR7209532_trim.fastq -SRR7209532.sam
3)Sort and convert SAM to BAM
module load SAMtools/1.10-GCC-8.3.0
samtools sort -@ 8 -o SRR7209532.bam RR7209532.sam
4)Assemble transcripts for each sample using StringTie
module load StringTie/2.1.1-GCC-8.3.0
stringtie -p 8 -G $chandra1/UNIL_Sinv_3.0/chr16.SB.NCBI_v3.4.gtf -o SRR7209534.gtf -l SRR7209532 SRR7209534.bam
My Results:
head SRR7209534.gtf
stringtie -p 8 -G /scratch/sab99204/Chandra/UNIL_Sinv_3.0/chr16.SB.NCBI_v3.4.gtf -oSRR7209534.gtf -l SRR7209532 SRR7209534.bam
StringTie version 2.1.1
It seems to just be printing my command in the ".gtf", can anoyone assist with this. I am not sure what to do. There is no error its just not working they way it should. If you need any other info please let me know!
it is difficult to guess what went wrong with the information furnished in OP. First guess is to check if chromosome representation in reference file and annotation file (gtf) are same (for eg. 1 vs chr1). Try to load bam in viewers such as IGV and navigate to region of interest and you should be seeing reads and other information visually. If you can see the reads and other relevant information, check your function to generate gtf.