Question: Genome guided assembly using hisat2 and StringTie
gravatar for Bioinfonext
3.5 years ago by
Bioinfonext240 wrote:

I map pair end reads to genome using Hisat2 and sam file was sort and converted in bam file.

After that I used this command for StringTie assembly:

/home/yog/software/stringtie-1.3.2.Linux_x86_64/stringtie -p 8 -G gene.gtf -o assembly.gtf -m 500 -v map.bam

It creates these following files:

1) assembly.gtf

2) t_data_ctab

3) i2t_ctab

4) i_data_ctab

5) e2t_ctab

6) e_data_ctab

then through gffread I extracted assembled fasta sequences, using reference.fasta

/gffread assembly.gtf -w transcript.fasta -g reference.fasta

Is it the right way to do genome-guided assembly using StringTie?

Can I get assembled fasta sequence directly from the above stringTie command?

Thanks in advance

rna-seq • 1.7k views
ADD COMMENTlink modified 3.4 years ago • written 3.5 years ago by Bioinfonext240

Hi, I am waiting for anyone using Hisat2 and StringTie together.


ADD REPLYlink written 3.4 years ago by Bioinfonext240
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