Hi Biostars Community,
I struggle with running the script extract_splice_sites.py Sbicolor_313_v3.1.gene.gtf > Sbicolor_313_v3.1.splicesites.txt) for extracting the splice sites from my gene annotation file. I was initially advidsed to convert my gene annotation file (Sbicolor_313_v3.1.gff3) to gtf format using gffread script, but still the script did not run. I really have no idea where the problem lies in the script. Please help!
Another problem I have is how to view the output file of HISAT. When I ran HISAT (hisat2 -p 8 -x Sbicolor_313_v3.0.index -1 RSL200mMMn0_R1_paired.fastq -2 RSL200mMmM0_R2_paired.fastq -S RSL200mMMn0.sam | samtools -bS -> RSL200mMMn0.bam) directly after creating the index files from my sorghum (Sbicolor_313_v3.0) genome, I was unable to view or locate my HISAT output file. How does one view the HISAT output file? Is there a command/script for viewing HISAT output files to see how many reads mapped?
I am still new in this field - thanks. Lekgolwa
Where did you get
extract_splice_sites.py? Do you get an error when you run it? What does your command look like?
->how you're trying to create the output file in your HISAT command? If you have a bam file you can view it with