HiSat2 and StringTie! -StringTie empty GTF file
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Entering edit mode
3 months ago
Sabrina • 0

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!

transcript assembly hisat2 stringtie DNA • 203 views
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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.

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